rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.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,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse 25320,SRR25810878,SRX21533024,SRS18745490,SRP457576,PRJNA1010780,Effect of egr3 knockout on gene expression of dissected zebrafish hearts,GSE241935,Transcriptome Analysis,To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf. We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS. Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12µl of RNase free water. Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples. 1. Boezio G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571,,pubmed:38748804,,egr3 wild type siblings 2,GSM7745909,,source name:Heart|tissue:Heart|genotype:bns577+/+|geo loc name:missing|collection date:missing,egr3 wild type siblings 2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al. Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts,Heart,,Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.,,tissue:Heart|genotype:bns577+/+,GSM7745909,GSM7745909: egr3 wild type siblings 2; Danio rerio; RNA Seq,GSM7745909 r1,GSM7745909,1,Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP457576,,loader:fastq load.py,E22_3626_Lib_Agatha_egr3_WT2_R1.fastq.gz,fastq,3473319384.0,49279465.0,GSM7745909 r1,0:70.48,A:943794847;C:792135324;G:792042625;T:945083925;N:262663,70,,,,943794847,792135324,792042625,945083925,262663,SRX21533024,SRS18745490,SRA1702458,MPI for heart and lung research,MPI for heart and lung research,1,0.68549,,0.04588,,0.76865,,0.44964,,71,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2023-08-30,Undetermined,Undetermined,Heart,Cardiovascular System 25321,SRR25810879,SRX21533023,SRS18745489,SRP457576,PRJNA1010780,Effect of egr3 knockout on gene expression of dissected zebrafish hearts,GSE241935,Transcriptome Analysis,To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf. We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS. Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12µl of RNase free water. Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples. 1. Boezio G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571,,pubmed:38748804,,egr3 wild type siblings 1,GSM7745908,,source name:Heart|tissue:Heart|genotype:bns577+/+|geo loc name:missing|collection date:missing,egr3 wild type siblings 1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al. Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts,Heart,,Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.,,tissue:Heart|genotype:bns577+/+,GSM7745908,GSM7745908: egr3 wild type siblings 1; Danio rerio; RNA Seq,GSM7745908 r1,GSM7745908,1,Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP457576,,loader:fastq load.py,E22_3626_Lib_Agatha_egr3_WT1_R1.fastq.gz,fastq,3909248616.0,55045571.0,GSM7745908 r1,0:71.02,A:1048107387;C:905014546;G:907455489;T:1048528690;N:142504,71,,,,1048107387,905014546,907455489,1048528690,142504,SRX21533023,SRS18745489,SRA1702458,MPI for heart and lung research,MPI for heart and lung research,1,0.94958,,0.06298,,0.74819,,0.45762,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2023-08-30,Undetermined,Undetermined,Heart,Cardiovascular System 25322,SRR25810880,SRX21533022,SRS18745488,SRP457576,PRJNA1010780,Effect of egr3 knockout on gene expression of dissected zebrafish hearts,GSE241935,Transcriptome Analysis,To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf. We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS. Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12µl of RNase free water. Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples. 1. Boezio G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571,,pubmed:38748804,,egr3 mutants 2,GSM7745907,,source name:Heart|tissue:Heart|genotype:bns577 / |geo loc name:missing|collection date:missing,egr3 mutants 2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al. Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts,Heart,,Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.,,tissue:Heart|genotype:bns577 / ,GSM7745907,GSM7745907: egr3 mutants 2; Danio rerio; RNA Seq,GSM7745907 r1,GSM7745907,1,Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP457576,,loader:fastq load.py,E22_3626_Lib_Agatha_egr3_Mut2_R1.fastq.gz,fastq,3432675258.0,48483287.0,GSM7745907 r1,0:70.80,A:925832958;C:788551205;G:790129536;T:927993012;N:168547,70,,,,925832958,788551205,790129536,927993012,168547,SRX21533022,SRS18745488,SRA1702458,MPI for heart and lung research,MPI for heart and lung research,1,0.75652,,0.04046,,0.76455,,0.46333,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2023-08-30,Undetermined,Undetermined,Heart,Cardiovascular System 25323,SRR25810881,SRX21533021,SRS18745487,SRP457576,PRJNA1010780,Effect of egr3 knockout on gene expression of dissected zebrafish hearts,GSE241935,Transcriptome Analysis,To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf. We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS. Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12µl of RNase free water. Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples. 1. Boezio G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571,,pubmed:38748804,,egr3 mutants 1,GSM7745906,,source name:Heart|tissue:Heart|genotype:bns577 / |geo loc name:missing|collection date:missing,egr3 mutants 1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al. Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts,Heart,,Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.,,tissue:Heart|genotype:bns577 / ,GSM7745906,GSM7745906: egr3 mutants 1; Danio rerio; RNA Seq,GSM7745906 r1,GSM7745906,1,Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP457576,,loader:fastq load.py,E22_3626_Lib_Agatha_egr3_Mut1_R1.fastq.gz,fastq,3838969347.0,54545950.0,GSM7745906 r1,0:70.38,A:1016913415;C:902500250;G:903033204;T:1016194618;N:327860,70,,,,1016913415,902500250,903033204,1016194618,327860,SRX21533021,SRS18745487,SRA1702458,MPI for heart and lung research,MPI for heart and lung research,1,0.9511,,0.05017,,0.75341,,0.47152,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2023-08-30,Undetermined,Undetermined,Heart,Cardiovascular System 49850,SRR8883829,SRX5669659,SRS4612528,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,148 2 E12 KOcxcl12a 6 reseq,GSM3719057,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,148 2 E12 KOcxcl12a 6 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719057,GSM3719057: 148 2 E12 KOcxcl12a 6 reseq; Danio rerio; RNA Seq,GSM3719057,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719057,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,148-2-E12-KOcxcl12a-6_reseq_all_lanes_R1.fastq.gz,fastq,763065205.0,10372479.0,GSM3719057 r1,0:73.57 1:0,A:179985921;C:199425581;G:205920814;T:177110327;N:622562,73,0,,,179985921,199425581,205920814,177110327,622562,SRX5669659,SRS4612528,SRA798477,GEO,University of Oxford,1,0.93161,,0.2297,,0.75684,,0.64613,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49851,SRR8883828,SRX5669658,SRS4612527,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,147 2 E11 KOcxcl12a 5 reseq,GSM3719056,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,147 2 E11 KOcxcl12a 5 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719056,GSM3719056: 147 2 E11 KOcxcl12a 5 reseq; Danio rerio; RNA Seq,GSM3719056,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719056,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,147-2-E11-KOcxcl12a-5_reseq_all_lanes_R1.fastq.gz,fastq,777154556.0,10544824.0,GSM3719056 r1,0:73.70 1:0,A:182318789;C:204282719;G:210781481;T:179272833;N:498734,73,0,,,182318789,204282719,210781481,179272833,498734,SRX5669658,SRS4612527,SRA798477,GEO,University of Oxford,1,0.94256,,0.25229,,0.76781,,0.67336,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49852,SRR8883827,SRX5669657,SRS4612526,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,146 2 E10 KOcxcl12a 4 reseq,GSM3719055,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,146 2 E10 KOcxcl12a 4 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719055,GSM3719055: 146 2 E10 KOcxcl12a 4 reseq; Danio rerio; RNA Seq,GSM3719055,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719055,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,146-2-E10-KOcxcl12a-4_reseq_all_lanes_R1.fastq.gz,fastq,893756036.0,12231836.0,GSM3719055 r1,0:73.07 1:0,A:208987215;C:235365706;G:243090724;T:205234077;N:1078314,73,0,,,208987215,235365706,243090724,205234077,1078314,SRX5669657,SRS4612526,SRA798477,GEO,University of Oxford,1,0.93675,,0.21776,,0.76597,,0.63391,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49853,SRR8883826,SRX5669656,SRS4612525,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,145 2 E09 KOcxcl12a 3 reseq,GSM3719054,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,145 2 E09 KOcxcl12a 3 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719054,GSM3719054: 145 2 E09 KOcxcl12a 3 reseq; Danio rerio; RNA Seq,GSM3719054,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719054,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,145-2-E09-KOcxcl12a-3_reseq_all_lanes_R1.fastq.gz,fastq,850857048.0,11668488.0,GSM3719054 r1,0:72.92 1:0,A:205769666;C:217594988;G:223805195;T:202463052;N:1224147,72,0,,,205769666,217594988,223805195,202463052,1224147,SRX5669656,SRS4612525,SRA798477,GEO,University of Oxford,1,0.92738,,0.2566,,0.75152,,0.65144,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49854,SRR8883825,SRX5669655,SRS4612524,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,144 2 E08 KOcxcl12a 2 reseq,GSM3719053,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,144 2 E08 KOcxcl12a 2 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719053,GSM3719053: 144 2 E08 KOcxcl12a 2 reseq; Danio rerio; RNA Seq,GSM3719053,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719053,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,144-2-E08-KOcxcl12a-2_reseq_all_lanes_R1.fastq.gz,fastq,898577334.0,12271421.0,GSM3719053 r1,0:73.23 1:0,A:209765901;C:237376777;G:244548553;T:205953258;N:932845,73,0,,,209765901,237376777,244548553,205953258,932845,SRX5669655,SRS4612524,SRA798477,GEO,University of Oxford,1,0.94312,,0.22115,,0.75751,,0.63782,,72,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49855,SRR8883824,SRX5669654,SRS4612523,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,143 2 E07 KOcxcl12a 1 reseq,GSM3719052,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,143 2 E07 KOcxcl12a 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719052,GSM3719052: 143 2 E07 KOcxcl12a 1 reseq; Danio rerio; RNA Seq,GSM3719052,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719052,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,143-2-E07-KOcxcl12a-1_reseq_all_lanes_R1.fastq.gz,fastq,642191206.0,8724687.0,GSM3719052 r1,0:73.61 1:0,A:148702964;C:170638392;G:176459501;T:145895525;N:494824,73,0,,,148702964,170638392,176459501,145895525,494824,SRX5669654,SRS4612523,SRA798477,GEO,University of Oxford,1,0.93805,,0.20319,,0.76203,,0.65533,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49856,SRR8883823,SRX5669653,SRS4612522,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,142 2 E06 KOcxcl12a ctr 3 reseq,GSM3719051,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,142 2 E06 KOcxcl12a ctr 3 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719051,GSM3719051: 142 2 E06 KOcxcl12a ctr 3 reseq; Danio rerio; RNA Seq,GSM3719051,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719051,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,142-2-E06-KOcxcl12a-ctr-3_reseq_all_lanes_R1.fastq.gz,fastq,913646709.0,12532356.0,GSM3719051 r1,0:72.90 1:0,A:210664396;C:243042644;G:251444631;T:207071337;N:1423701,72,0,,,210664396,243042644,251444631,207071337,1423701,SRX5669653,SRS4612522,SRA798477,GEO,University of Oxford,1,0.93582,,0.21132,,0.7669,,0.65882,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49857,SRR8883822,SRX5669652,SRS4612521,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,141 2 E05 KOcxcl12a ctr 2 reseq,GSM3719050,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,141 2 E05 KOcxcl12a ctr 2 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719050,GSM3719050: 141 2 E05 KOcxcl12a ctr 2 reseq; Danio rerio; RNA Seq,GSM3719050,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719050,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,141-2-E05-KOcxcl12a-ctr-2_reseq_all_lanes_R1.fastq.gz,fastq,698256933.0,9557079.0,GSM3719050 r1,0:73.06 1:0,A:165636445;C:181576831;G:187431558;T:162693862;N:918237,73,0,,,165636445,181576831,187431558,162693862,918237,SRX5669652,SRS4612521,SRA798477,GEO,University of Oxford,1,0.92623,,0.20301,,0.75562,,0.58643,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49858,SRR8883821,SRX5669651,SRS4612520,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,140 2 E04 KOcxcl12a ctr 1 reseq,GSM3719049,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,140 2 E04 KOcxcl12a ctr 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719049,GSM3719049: 140 2 E04 KOcxcl12a ctr 1 reseq; Danio rerio; RNA Seq,GSM3719049,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719049,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,140-2-E04-KOcxcl12a-ctr-1_reseq_all_lanes_R1.fastq.gz,fastq,824049635.0,11240750.0,GSM3719049 r1,0:73.31 1:0,A:195127513;C:214512790;G:222034432;T:191506323;N:868577,73,0,,,195127513,214512790,222034432,191506323,868577,SRX5669651,SRS4612520,SRA798477,GEO,University of Oxford,1,0.93289,,0.20393,,0.75749,,0.60814,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49859,SRR8883820,SRX5669650,SRS4612519,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,130 2 D06 KOsema3fb tbx18 1 reseq,GSM3719048,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,130 2 D06 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719048,GSM3719048: 130 2 D06 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719048,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719048,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,130-2-D06-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,1162709924.0,15925191.0,GSM3719048 r1,0:73.01 1:0,A:289120225;C:287784856;G:301546291;T:282206243;N:2052309,73,0,,,289120225,287784856,301546291,282206243,2052309,SRX5669650,SRS4612519,SRA798477,GEO,University of Oxford,1,0.7653,,0.25001,,0.98997,,0.83422,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49860,SRR8883819,SRX5669649,SRS4612518,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,124 2 C12 KOsema3fb tbx18 1 reseq,GSM3719047,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,124 2 C12 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719047,GSM3719047: 124 2 C12 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719047,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719047,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,124-2-C12-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,299825780.0,4022960.0,GSM3719047 r1,0:74.53 1:0,A:68392314;C:78125239;G:84196045;T:69093198;N:18984,74,0,,,68392314,78125239,84196045,69093198,18984,SRX5669649,SRS4612518,SRA798477,GEO,University of Oxford,1,0.74846,,0.27048,,0.99557,,0.70087,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49861,SRR8883818,SRX5669648,SRS4612517,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,123 2 C11 KOsema3fb tbx18 1 reseq,GSM3719046,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,123 2 C11 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719046,GSM3719046: 123 2 C11 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719046,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719046,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,123-2-C11-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,295959651.0,3971786.0,GSM3719046 r1,0:74.52 1:0,A:77279704;C:70402673;G:74373147;T:73882710;N:21417,74,0,,,77279704,70402673,74373147,73882710,21417,SRX5669648,SRS4612517,SRA798477,GEO,University of Oxford,1,0.82981,,0.14333,,0.99758,,0.91205,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49862,SRR8883817,SRX5669647,SRS4612516,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,119 2 C07 KOsema3fb tbx18 1 reseq,GSM3719045,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,119 2 C07 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719045,GSM3719045: 119 2 C07 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719045,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719045,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,119-2-C07-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,264496882.0,3548156.0,GSM3719045 r1,0:74.54 1:0,A:75579264;C:55698110;G:58441353;T:74755905;N:22250,74,0,,,75579264,55698110,58441353,74755905,22250,SRX5669647,SRS4612516,SRA798477,GEO,University of Oxford,1,0.80888,,0.37987,,0.98039,,0.91771,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49863,SRR8883816,SRX5669646,SRS4612515,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,113 2 C01 KOsema3fb tbx18 1 reseq,GSM3719044,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,113 2 C01 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719044,GSM3719044: 113 2 C01 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719044,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719044,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,113-2-C01-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,900078149.0,12264833.0,GSM3719044 r1,0:73.39 1:0,A:219770321;C:225774705;G:235824823;T:217584908;N:1123392,73,0,,,219770321,225774705,235824823,217584908,1123392,SRX5669646,SRS4612515,SRA798477,GEO,University of Oxford,1,0.7672,,0.32569,,0.9811,,0.69383,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49864,SRR8883815,SRX5669645,SRS4612514,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,109 2 B08 KOsema3fb tbx18 1 reseq,GSM3719043,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,109 2 B08 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719043,GSM3719043: 109 2 B08 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719043,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719043,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,109-2-B08-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,1184134969.0,16001572.0,GSM3719043 r1,0:74.00 1:0,A:349230233;C:244528650;G:253057471;T:336773385;N:545230,74,0,,,349230233,244528650,253057471,336773385,545230,SRX5669645,SRS4612514,SRA798477,GEO,University of Oxford,1,0.88887,,0.09304,,0.99348,,0.98604,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49865,SRR8883814,SRX5669644,SRS4612513,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,106 2 B05 KOsema3fb tbx18 1 reseq,GSM3719042,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,106 2 B05 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719042,GSM3719042: 106 2 B05 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719042,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719042,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,106-2-B05-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,1419090881.0,19189635.0,GSM3719042 r1,0:73.95 1:0,A:373650546;C:329135514;G:344779857;T:370771195;N:753769,73,0,,,373650546,329135514,344779857,370771195,753769,SRX5669644,SRS4612513,SRA798477,GEO,University of Oxford,1,0.80666,,0.39497,,0.98307,,0.82884,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49866,SRR8883813,SRX5669643,SRS4612512,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,102 2 B01 KOsema3fb tbx18 1 reseq,GSM3719041,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,102 2 B01 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719041,GSM3719041: 102 2 B01 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719041,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719041,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,102-2-B01-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,792286694.0,10728522.0,GSM3719041 r1,0:73.85 1:0,A:208005708;C:185723186;G:192254855;T:205724930;N:578015,73,0,,,208005708,185723186,192254855,205724930,578015,SRX5669643,SRS4612512,SRA798477,GEO,University of Oxford,1,0.83885,,0.20822,,0.93385,,0.55626,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49867,SRR8883812,SRX5669642,SRS4612511,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,099 2 A10 KOsema3fb tbx18 1 reseq,GSM3719040,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,099 2 A10 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719040,GSM3719040: 099 2 A10 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719040,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719040,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,099-2-A10-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,1259856601.0,17276596.0,GSM3719040 r1,0:72.92 1:0,A:327815757;C:292688430;G:309183926;T:327561592;N:2606896,72,0,,,327815757,292688430,309183926,327561592,2606896,SRX5669642,SRS4612511,SRA798477,GEO,University of Oxford,1,0.75716,,0.21591,,0.98545,,0.88552,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49868,SRR8883811,SRX5669641,SRS4612510,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,094 2 A04 KOsema3fb tbx18 1 reseq,GSM3719039,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,094 2 A04 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719039,GSM3719039: 094 2 A04 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719039,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719039,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,094-2-A04-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,1393707010.0,19037650.0,GSM3719039 r1,0:73.21 1:0,A:419699742;C:277700843;G:287769215;T:406877217;N:1659993,73,0,,,419699742,277700843,287769215,406877217,1659993,SRX5669641,SRS4612510,SRA798477,GEO,University of Oxford,1,0.89441,,0.12858,,0.98875,,0.97807,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49869,SRR8883810,SRX5669640,SRS4612509,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,091 2 A01 KOsema3fb tbx18 1 reseq,GSM3719038,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,091 2 A01 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719038,GSM3719038: 091 2 A01 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719038,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719038,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,091-2-A01-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,1312071784.0,17781006.0,GSM3719038 r1,0:73.79 1:0,A:366473328;C:287833987;G:300280345;T:356559257;N:924867,73,0,,,366473328,287833987,300280345,356559257,924867,SRX5669640,SRS4612509,SRA798477,GEO,University of Oxford,1,0.84829,,0.13012,,0.99239,,0.95627,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49870,SRR8883809,SRX5669639,SRS4612508,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,089 1 H11 KOsema3fb tbx18 1 reseq,GSM3719037,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,089 1 H11 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719037,GSM3719037: 089 1 H11 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719037,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719037,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,089-1-H11-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,457617610.0,6259652.0,GSM3719037 r1,0:73.11 1:0,A:102784836;C:123244653;G:128352318;T:102443570;N:792233,73,0,,,102784836,123244653,128352318,102443570,792233,SRX5669639,SRS4612508,SRA798477,GEO,University of Oxford,1,0.41215,,0.14696,,0.99474,,0.79701,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49871,SRR8883808,SRX5669638,SRS4612507,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,088 1 H10 KOsema3fb tbx18 1 reseq,GSM3719036,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,088 1 H10 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719036,GSM3719036: 088 1 H10 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719036,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719036,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,088-1-H10-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,1045203718.0,14235004.0,GSM3719036 r1,0:73.42 1:0,A:245506754;C:275986612;G:284480834;T:238462022;N:767496,73,0,,,245506754,275986612,284480834,238462022,767496,SRX5669638,SRS4612507,SRA798477,GEO,University of Oxford,1,0.78399,,0.27279,,0.96171,,0.64393,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49872,SRR8883807,SRX5669637,SRS4612506,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,085 1 H07 KOsema3fb tbx18 1 reseq,GSM3719035,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,085 1 H07 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719035,GSM3719035: 085 1 H07 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719035,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719035,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,085-1-H07-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,994545532.0,13515281.0,GSM3719035 r1,0:73.59 1:0,A:251733790;C:239766112;G:249497960;T:252514979;N:1032691,73,0,,,251733790,239766112,249497960,252514979,1032691,SRX5669637,SRS4612506,SRA798477,GEO,University of Oxford,1,0.76592,,0.33384,,0.97488,,0.6386,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49873,SRR8883806,SRX5669636,SRS4612505,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,083 1 H05 KOsema3fb tbx18 1 reseq,GSM3719034,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,083 1 H05 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719034,GSM3719034: 083 1 H05 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719034,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719034,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,083-1-H05-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,1559012386.0,21214346.0,GSM3719034 r1,0:73.49 1:0,A:377233697;C:392858147;G:413542175;T:373251234;N:2127133,73,0,,,377233697,392858147,413542175,373251234,2127133,SRX5669636,SRS4612505,SRA798477,GEO,University of Oxford,1,0.76884,,0.25038,,0.99304,,0.82504,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49874,SRR8883805,SRX5669635,SRS4612504,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,080 1 H02 KOsema3fb tbx18 1 reseq,GSM3719033,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,080 1 H02 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719033,GSM3719033: 080 1 H02 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719033,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719033,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,080-1-H02-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,1858691358.0,25414284.0,GSM3719033 r1,0:73.14 1:0,A:476963365;C:445987754;G:466752717;T:466112688;N:2874834,73,0,,,476963365,445987754,466752717,466112688,2874834,SRX5669635,SRS4612504,SRA798477,GEO,University of Oxford,1,0.68992,,0.2736,,0.982,,0.82915,,59,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49875,SRR8883804,SRX5669634,SRS4612503,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,075 1 G09 KOsema3fb tbx18 1 reseq,GSM3719032,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,075 1 G09 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719032,GSM3719032: 075 1 G09 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719032,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719032,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,075-1-G09-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,268112375.0,3598019.0,GSM3719032 r1,0:74.52 1:0,A:65372074;C:67071915;G:71029798;T:64617919;N:20669,74,0,,,65372074,67071915,71029798,64617919,20669,SRX5669634,SRS4612503,SRA798477,GEO,University of Oxford,1,0.67884,,0.23576,,0.98717,,0.82171,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49876,SRR8883803,SRX5669633,SRS4612502,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,071 1 G05 KOsema3fb tbx18 1 reseq,GSM3719031,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,071 1 G05 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719031,GSM3719031: 071 1 G05 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719031,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719031,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,071-1-G05-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,828746401.0,11302582.0,GSM3719031 r1,0:73.32 1:0,A:229221425;C:183717145;G:190544172;T:224163771;N:1099888,73,0,,,229221425,183717145,190544172,224163771,1099888,SRX5669633,SRS4612502,SRA798477,GEO,University of Oxford,1,0.81759,,0.13538,,0.89315,,0.45516,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49877,SRR8883802,SRX5669631,SRS4612500,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,070 1 G04 KOsema3fb tbx18 1 reseq,GSM3719030,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,070 1 G04 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719030,GSM3719030: 070 1 G04 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719030,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719030,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,070-1-G04-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,106414765.0,1428334.0,GSM3719030 r1,0:74.50 1:0,A:29193564;C:23683625;G:26548630;T:26978197;N:10749,74,0,,,29193564,23683625,26548630,26978197,10749,SRX5669631,SRS4612500,SRA798477,GEO,University of Oxford,1,0.4816,,0.11056,,0.99176,,0.92847,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49878,SRR8883801,SRX5669630,SRS4612499,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,063 1 F09 KOsema3fb tbx18 1 reseq,GSM3719029,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,063 1 F09 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719029,GSM3719029: 063 1 F09 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719029,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719029,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,063-1-F09-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,1418543217.0,19449719.0,GSM3719029 r1,0:72.93 1:0,A:337365498;C:374610477;G:384311752;T:320594026;N:1661464,72,0,,,337365498,374610477,384311752,320594026,1661464,SRX5669630,SRS4612499,SRA798477,GEO,University of Oxford,1,0.72075,,0.19017,,0.94852,,0.65802,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49879,SRR8883800,SRX5669629,SRS4612498,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,059 1 F05 KOsema3fb tbx18 1 reseq,GSM3719028,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,059 1 F05 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719028,GSM3719028: 059 1 F05 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719028,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719028,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,059-1-F05-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,628014958.0,8461681.0,GSM3719028 r1,0:74.22 1:0,A:169712705;C:143325768;G:146633959;T:168144033;N:198493,74,0,,,169712705,143325768,146633959,168144033,198493,SRX5669629,SRS4612498,SRA798477,GEO,University of Oxford,1,0.88635,,0.30859,,0.94945,,0.51713,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49880,SRR8883799,SRX5669628,SRS4612497,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,058 1 F04 KOsema3fb tbx18 1 reseq,GSM3719027,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,058 1 F04 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719027,GSM3719027: 058 1 F04 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719027,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719027,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,058-1-F04-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,1132466748.0,15352198.0,GSM3719027 r1,0:73.77 1:0,A:287483650;C:275728373;G:284236125;T:284105636;N:912964,73,0,,,287483650,275728373,284236125,284105636,912964,SRX5669628,SRS4612497,SRA798477,GEO,University of Oxford,1,0.85479,,0.29074,,0.94787,,0.64434,,72,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49881,SRR8883798,SRX5669627,SRS4612496,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,054 1 E12 KOsema3fb tbx18 1 reseq,GSM3719026,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,054 1 E12 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719026,GSM3719026: 054 1 E12 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719026,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719026,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,054-1-E12-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,1629595640.0,22258229.0,GSM3719026 r1,0:73.21 1:0,A:413072064;C:401501367;G:412845503;T:400653209;N:1523497,73,0,,,413072064,401501367,412845503,400653209,1523497,SRX5669627,SRS4612496,SRA798477,GEO,University of Oxford,1,0.80047,,0.25253,,0.95489,,0.577,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49882,SRR8883797,SRX5669626,SRS4612495,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,053 1 E11 KOsema3fb tbx18 1 reseq,GSM3719025,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,053 1 E11 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719025,GSM3719025: 053 1 E11 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719025,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719025,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,053-1-E11-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,1486706263.0,20480281.0,GSM3719025 r1,0:72.59 1:0,A:371137003;C:370842438;G:377947483;T:365166253;N:1613086,72,0,,,371137003,370842438,377947483,365166253,1613086,SRX5669626,SRS4612495,SRA798477,GEO,University of Oxford,1,0.90527,,0.12233,,0.92535,,0.49493,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49883,SRR8883796,SRX5669625,SRS4612494,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,052 1 E10 KOsema3fb tbx18 1 reseq,GSM3719024,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,052 1 E10 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719024,GSM3719024: 052 1 E10 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719024,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719024,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,052-1-E10-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,1081235863.0,14851741.0,GSM3719024 r1,0:72.80 1:0,A:270268231;C:269602955;G:274380996;T:265977713;N:1005968,72,0,,,270268231,269602955,274380996,265977713,1005968,SRX5669625,SRS4612494,SRA798477,GEO,University of Oxford,1,0.9403,,0.05017,,0.90412,,0.49703,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49884,SRR8883795,SRX5669624,SRS4612493,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,046 1 E03 KOsema3fb tbx18 1 reseq,GSM3719023,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,046 1 E03 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719023,GSM3719023: 046 1 E03 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719023,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719023,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,046-1-E03-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,1601412676.0,21633821.0,GSM3719023 r1,0:74.02 1:0,A:429878446;C:367923948;G:377956363;T:424839589;N:814330,74,0,,,429878446,367923948,377956363,424839589,814330,SRX5669624,SRS4612493,SRA798477,GEO,University of Oxford,1,0.87207,,0.23243,,0.9177,,0.55272,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49885,SRR8883794,SRX5669623,SRS4612492,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,045 1 E02 KOsema3fb tbx18 1 reseq,GSM3719022,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,045 1 E02 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719022,GSM3719022: 045 1 E02 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719022,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719022,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,045-1-E02-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,1325652418.0,18022884.0,GSM3719022 r1,0:73.55 1:0,A:370796542;C:292964387;G:300362786;T:360541988;N:986715,73,0,,,370796542,292964387,300362786,360541988,986715,SRX5669623,SRS4612492,SRA798477,GEO,University of Oxford,1,0.82878,,0.13178,,0.99387,,0.97164,,73,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49886,SRR8883793,SRX5669595,SRS4612464,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,042 1 D11 KOsema3fb tbx18 1 reseq,GSM3719021,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,042 1 D11 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719021,GSM3719021: 042 1 D11 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719021,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719021,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,042-1-D11-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,181531543.0,2441046.0,GSM3719021 r1,0:74.37 1:0,A:47878030;C:43004057;G:45184887;T:45333065;N:131504,74,0,,,47878030,43004057,45184887,45333065,131504,SRX5669595,SRS4612464,SRA798477,GEO,University of Oxford,1,0.66305,,0.32574,,0.97206,,0.69463,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49887,SRR8883792,SRX5669594,SRS4612463,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,038 1 D06 KOsema3fb tbx18 1 reseq,GSM3719020,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,038 1 D06 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719020,GSM3719020: 038 1 D06 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719020,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719020,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,038-1-D06-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,168156139.0,2261594.0,GSM3719020 r1,0:74.35 1:0,A:42354992;C:41900555;G:44340628;T:39432087;N:127877,74,0,,,42354992,41900555,44340628,39432087,127877,SRX5669594,SRS4612463,SRA798477,GEO,University of Oxford,1,0.60767,,0.21853,,0.9903,,0.79842,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49888,SRR8883791,SRX5669593,SRS4612462,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,033 1 D01 KOsema3fb tbx18 1 reseq,GSM3719019,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,033 1 D01 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719019,GSM3719019: 033 1 D01 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719019,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719019,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,033-1-D01-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,1805852084.0,24752177.0,GSM3719019 r1,0:72.96 1:0,A:484272872;C:416872457;G:427392429;T:474646299;N:2668027,72,0,,,484272872,416872457,427392429,474646299,2668027,SRX5669593,SRS4612462,SRA798477,GEO,University of Oxford,1,0.86769,,0.24446,,0.90954,,0.52112,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49889,SRR8883790,SRX5669592,SRS4612461,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,031 1 C11 KOsema3fb tbx18 1 reseq,GSM3719018,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,031 1 C11 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719018,GSM3719018: 031 1 C11 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719018,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719018,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,031-1-C11-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,258591680.0,3472457.0,GSM3719018 r1,0:74.47 1:0,A:64790229;C:64970309;G:69416663;T:59350946;N:63533,74,0,,,64790229,64970309,69416663,59350946,63533,SRX5669592,SRS4612461,SRA798477,GEO,University of Oxford,1,0.6005,,0.17126,,0.99139,,0.81853,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49890,SRR8883789,SRX5669591,SRS4612460,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,027 1 C06 KOsema3fb tbx18 1 reseq,GSM3719017,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,027 1 C06 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719017,GSM3719017: 027 1 C06 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719017,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719017,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,027-1-C06-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,1296475193.0,17694501.0,GSM3719017 r1,0:73.27 1:0,A:351327244;C:293439849;G:302900890;T:347251212;N:1555998,73,0,,,351327244,293439849,302900890,347251212,1555998,SRX5669591,SRS4612460,SRA798477,GEO,University of Oxford,1,0.85074,,0.26491,,0.90749,,0.56504,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49891,SRR8883788,SRX5669590,SRS4612459,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,026 1 C05 KOsema3fb tbx18 1 reseq,GSM3719016,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,026 1 C05 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719016,GSM3719016: 026 1 C05 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719016,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719016,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,026-1-C05-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,284767981.0,3826742.0,GSM3719016 r1,0:74.42 1:0,A:72059849;C:70126842;G:73586073;T:68935800;N:59417,74,0,,,72059849,70126842,73586073,68935800,59417,SRX5669590,SRS4612459,SRA798477,GEO,University of Oxford,1,0.64774,,0.40257,,0.98926,,0.81073,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49892,SRR8883787,SRX5669589,SRS4612458,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,023 1 C02 KOsema3fb tbx18 1 reseq,GSM3719015,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,023 1 C02 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719015,GSM3719015: 023 1 C02 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719015,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719015,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,023-1-C02-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,350095216.0,4702156.0,GSM3719015 r1,0:74.45 1:0,A:86568719;C:87778353;G:93408696;T:82295750;N:43698,74,0,,,86568719,87778353,93408696,82295750,43698,SRX5669589,SRS4612458,SRA798477,GEO,University of Oxford,1,0.68061,,0.26106,,0.99308,,0.78108,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49893,SRR8883786,SRX5669588,SRS4612457,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,021 1 B12 KOsema3fb tbx18 1 reseq,GSM3719014,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,021 1 B12 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719014,GSM3719014: 021 1 B12 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719014,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719014,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,021-1-B12-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,244139057.0,3276020.0,GSM3719014 r1,0:74.52 1:0,A:57869172;C:62768357;G:66137806;T:57351114;N:12608,74,0,,,57869172,62768357,66137806,57351114,12608,SRX5669588,SRS4612457,SRA798477,GEO,University of Oxford,1,0.82069,,0.30044,,0.98835,,0.7106,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49894,SRR8883785,SRX5669587,SRS4612456,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,013 1 B03 KOsema3fb tbx18 1 reseq,GSM3719013,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,013 1 B03 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719013,GSM3719013: 013 1 B03 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719013,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719013,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,013-1-B03-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,300593693.0,4034452.0,GSM3719013 r1,0:74.51 1:0,A:71006915;C:76895402;G:83040096;T:69599791;N:51489,74,0,,,71006915,76895402,83040096,69599791,51489,SRX5669587,SRS4612456,SRA798477,GEO,University of Oxford,1,0.70351,,0.24566,,0.99405,,0.81062,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49895,SRR8883784,SRX5669586,SRS4612455,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,009 1 A11 KOsema3fb tbx18 1 reseq,GSM3719012,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,009 1 A11 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719012,GSM3719012: 009 1 A11 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719012,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719012,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,009-1-A11-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,390118139.0,5234216.0,GSM3719012 r1,0:74.53 1:0,A:107520990;C:85953937;G:90237162;T:106350398;N:55652,74,0,,,107520990,85953937,90237162,106350398,55652,SRX5669586,SRS4612455,SRA798477,GEO,University of Oxford,1,0.74505,,0.33293,,0.95219,,0.57072,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49896,SRR8883783,SRX5669585,SRS4612454,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,008 1 A10 KOsema3fb tbx18 1 reseq,GSM3719011,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,008 1 A10 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719011,GSM3719011: 008 1 A10 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719011,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719011,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,008-1-A10-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,229348931.0,3078894.0,GSM3719011 r1,0:74.49 1:0,A:58555603;C:55818636;G:59187704;T:55743030;N:43958,74,0,,,58555603,55818636,59187704,55743030,43958,SRX5669585,SRS4612454,SRA798477,GEO,University of Oxford,1,0.63109,,0.17996,,0.99417,,0.87477,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49897,SRR8883782,SRX5669584,SRS4612453,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,003 1 A05 KOsema3fb tbx18 1 reseq,GSM3719010,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,003 1 A05 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719010,GSM3719010: 003 1 A05 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719010,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719010,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,003-1-A05-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,346971595.0,4658492.0,GSM3719010 r1,0:74.48 1:0,A:90635619;C:83084783;G:88551844;T:84611362;N:87987,74,0,,,90635619,83084783,88551844,84611362,87987,SRX5669584,SRS4612453,SRA798477,GEO,University of Oxford,1,0.58325,,0.25436,,0.98498,,0.67358,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 49898,SRR8883781,SRX5669582,SRS4612451,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,001 1 A03 KOsema3fb tbx18 1 reseq,GSM3719009,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,001 1 A03 KOsema3fb tbx18 1 reseq,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719009,GSM3719009: 001 1 A03 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq,GSM3719009,,1,Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT,GEO Accession:GSM3719009,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP166782,,,001-1-A03-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz,fastq,903233066.0,12336870.0,GSM3719009 r1,0:73.21 1:0,A:236877184;C:210500125;G:221194577;T:232424088;N:2237092,73,0,,,236877184,210500125,221194577,232424088,2237092,SRX5669582,SRS4612451,SRA798477,GEO,University of Oxford,1,0.70527,,0.31845,,0.97997,,0.64502,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System 51309,SRR9903401,SRX6655218,SRS5216354,SRP217413,PRJNA526570,Cardiac neural crest contributes to cardiomyocytes in amniotes and heart regeneration in zebrafish,PRJNA526570,Whole Genome Sequencing,A gene expression analysis of neural crest contributions to zebrafish heart regeneration.,,,FAC sorted 21dpa GFP negative cells from adult Tg 4.9sox10:eGFP cardiac ventricles,21dpa Sox10negative,21dpa sox10 negative,,strain:Tg 4.9sox10:eGFP|dev stage:adult|sex:not applicable|tissue:adult ventricle|BioSampleModel:Model organism or animal,,,,,,,,,21dpa sox10 negative,Sox10 negative,Sox10 negative,Takara/Clontech SMART Seq V4 Ultra low Input RNAseq Kit using manufacturer's protocol,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP217413,,,21dpa_sox10neg_Rep1.fastq.gz 21dpa_sox10neg_Rep2.fastq.gz,fastq fastq,5676411900.0,113528238.0,21dpa sox10neg Rep1.fastq.gz,0:50,A:1633149451;C:1207650148;G:1213406307;T:1622182058;N:23936,50,,,,1633149451,1207650148,1213406307,1622182058,23936,SRX6655218,SRS5216354,SRA933745,California Institute of Technology|Biology and Biological Engineering,California Institute of Technology,1,0.88225,,0.11786,,0.78127,,0.52789,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2019-08-06,Adult,Adult,Heart,Cardiovascular System 51310,SRR9903402,SRX6655217,SRS5216353,SRP217413,PRJNA526570,Cardiac neural crest contributes to cardiomyocytes in amniotes and heart regeneration in zebrafish,PRJNA526570,Whole Genome Sequencing,A gene expression analysis of neural crest contributions to zebrafish heart regeneration.,,,FAC sorted 21dpa GFP positive cells from adult Tg 4.9sox10:eGFP cardiac ventricles,21dpa Sox10positive,21dpa sox10 positive,,strain:Tg 4.9sox10:eGFP|dev stage:adult|sex:not applicable|tissue:adult ventricle|BioSampleModel:Model organism or animal,,,,,,,,,21dpa sox10 positive,Sox10 positive,Sox10 positive,Takara/Clontech SMART Seq V4 Ultra low Input RNAseq Kit using manufacturer's protocol,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP217413,,,21dpa_sox10pos_Rep1.fastq.gz 21dpa_sox10pos_Rep2.fastq.gz,fastq fastq,5505584050.0,110111681.0,21dpa sox10pos Rep1.fastq.gz,0:50,A:1575542391;C:1178076405;G:1184130971;T:1567810031;N:24252,50,,,,1575542391,1178076405,1184130971,1567810031,24252,SRX6655217,SRS5216353,SRA933745,California Institute of Technology|Biology and Biological Engineering,California Institute of Technology,1,0.89136,,0.11182,,0.80649,,0.49369,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2019-08-06,Adult,Adult,Heart,Cardiovascular System 52976,SRR9622333,SRX6385177,SRS5044695,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,CoBFP333,GSM3912428,,source name:Adult zebrafish heart Uninjured BFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:BFP,CoBFP333,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Uninjured BFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:BFP,GSM3912428,GSM3912428: CoBFP333; Danio rerio; RNA Seq,GSM3912428,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912428,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1333.fastq.gz,fastq,1043783100.0,13917108.0,GSM3912428 r1,0:75 1:0,A:264029161;C:263617646;G:261888950;T:254205465;N:41878,75,0,,,264029161,263617646,261888950,254205465,41878,SRX6385177,SRS5044695,SRA915985,GEO,University of Bern,1,0.86382,,0.07728,,0.83792,,0.54248,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52977,SRR9622332,SRX6385176,SRS5044694,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,Ch317,GSM3912427,,source name:Adult zebrafish heart Uninjured RFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:RFP,Ch317,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Uninjured RFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:RFP,GSM3912427,GSM3912427: Ch317; Danio rerio; RNA Seq,GSM3912427,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912427,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1317.fastq.gz,fastq,973748550.0,12983314.0,GSM3912427 r1,0:75 1:0,A:248375971;C:244632945;G:244108158;T:236594598;N:36878,75,0,,,248375971,244632945,244108158,236594598,36878,SRX6385176,SRS5044694,SRA915985,GEO,University of Bern,1,0.85484,,0.08731,,0.84041,,0.52562,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52978,SRR9622331,SRX6385175,SRS5044693,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,Ch313,GSM3912426,,source name:Adult zebrafish heart Uninjured RFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:RFP,Ch313,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Uninjured RFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:RFP,GSM3912426,GSM3912426: Ch313; Danio rerio; RNA Seq,GSM3912426,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912426,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1313.fastq.gz,fastq,902474625.0,12032995.0,GSM3912426 r1,0:75 1:0,A:233742925;C:223473603;G:217976019;T:227248021;N:34057,75,0,,,233742925,223473603,217976019,227248021,34057,SRX6385175,SRS5044693,SRA915985,GEO,University of Bern,1,0.75654,,0.07592,,0.97877,,0.80602,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52979,SRR9622330,SRX6385174,SRS5044692,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,CICh281,GSM3912425,,source name:Adult zebrafish heart Cryoinjury RFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,CICh281,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Cryoinjury RFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,GSM3912425,GSM3912425: CICh281; Danio rerio; RNA Seq,GSM3912425,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912425,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1281.fastq.gz,fastq,1098083100.0,14641108.0,GSM3912425 r1,0:75 1:0,A:281532336;C:273824920;G:269232990;T:273451291;N:41563,75,0,,,281532336,273824920,269232990,273451291,41563,SRX6385174,SRS5044692,SRA915985,GEO,University of Bern,1,0.9319,,0.02768,,0.891,,0.55971,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52980,SRR9622329,SRX6385173,SRS5044691,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,CoBFP257,GSM3912424,,source name:Adult zebrafish heart Uninjured BFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:BFP,CoBFP257,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Uninjured BFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:BFP,GSM3912424,GSM3912424: CoBFP257; Danio rerio; RNA Seq,GSM3912424,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912424,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1257.fastq.gz,fastq,968650125.0,12915335.0,GSM3912424 r1,0:75 1:0,A:245690915;C:241347580;G:238158969;T:243415313;N:37348,75,0,,,245690915,241347580,238158969,243415313,37348,SRX6385173,SRS5044691,SRA915985,GEO,University of Bern,1,0.92368,,0.05908,,0.88316,,0.56213,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52981,SRR9622328,SRX6385172,SRS5044690,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,Ch249,GSM3912423,,source name:Adult zebrafish heart Uninjured RFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:RFP,Ch249,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Uninjured RFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:RFP,GSM3912423,GSM3912423: Ch249; Danio rerio; RNA Seq,GSM3912423,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912423,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1249.fastq.gz,fastq,1009794675.0,13463929.0,GSM3912423 r1,0:75 1:0,A:260146877;C:248118087;G:244258237;T:257231587;N:39887,75,0,,,260146877,248118087,244258237,257231587,39887,SRX6385172,SRS5044690,SRA915985,GEO,University of Bern,1,0.90314,,0.06804,,0.919,,0.57701,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52982,SRR9622327,SRX6385171,SRS5044689,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,Ch241,GSM3912422,,source name:Adult zebrafish heart Uninjured RFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:RFP,Ch241,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Uninjured RFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:RFP,GSM3912422,GSM3912422: Ch241; Danio rerio; RNA Seq,GSM3912422,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912422,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1241.fastq.gz,fastq,1109890200.0,14798536.0,GSM3912422 r1,0:75 1:0,A:279306864;C:278876734;G:275540725;T:276122445;N:43432,75,0,,,279306864,278876734,275540725,276122445,43432,SRX6385171,SRS5044689,SRA915985,GEO,University of Bern,1,0.92782,,0.0678,,0.85458,,0.57156,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52983,SRR9622326,SRX6385170,SRS5044688,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,CoBFP233,GSM3912421,,source name:Adult zebrafish heart Uninjured BFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:BFP,CoBFP233,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Uninjured BFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:BFP,GSM3912421,GSM3912421: CoBFP233; Danio rerio; RNA Seq,GSM3912421,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912421,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1233.fastq.gz,fastq,885089325.0,11801191.0,GSM3912421 r1,0:75 1:0,A:226315977;C:220280940;G:215727533;T:222731773;N:33102,75,0,,,226315977,220280940,215727533,222731773,33102,SRX6385170,SRS5044688,SRA915985,GEO,University of Bern,1,0.93542,,0.07677,,0.86145,,0.65301,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52984,SRR9622325,SRX6385169,SRS5044686,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,Ch225,GSM3912420,,source name:Adult zebrafish heart Uninjured RFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:RFP,Ch225,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Uninjured RFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:RFP,GSM3912420,GSM3912420: Ch225; Danio rerio; RNA Seq,GSM3912420,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912420,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1225.fastq.gz,fastq,1165189425.0,15535859.0,GSM3912420 r1,0:75 1:0,A:303228795;C:286063892;G:279312231;T:296539957;N:44550,75,0,,,303228795,286063892,279312231,296539957,44550,SRX6385169,SRS5044686,SRA915985,GEO,University of Bern,1,0.93956,,0.03123,,0.89309,,0.59448,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52985,SRR9622324,SRX6385168,SRS5044687,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,Ch217,GSM3912419,,source name:Adult zebrafish heart Uninjured RFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:RFP,Ch217,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Uninjured RFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:RFP,GSM3912419,GSM3912419: Ch217; Danio rerio; RNA Seq,GSM3912419,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912419,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1217.fastq.gz,fastq,1041721800.0,13889624.0,GSM3912419 r1,0:75 1:0,A:280775782;C:249795698;G:248228244;T:262882610;N:39466,75,0,,,280775782,249795698,248228244,262882610,39466,SRX6385168,SRS5044687,SRA915985,GEO,University of Bern,1,0.85832,,0.02792,,0.92415,,0.74437,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52986,SRR9622323,SRX6385167,SRS5044685,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,CoBFP209,GSM3912418,,source name:Adult zebrafish heart Uninjured BFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:BFP,CoBFP209,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Uninjured BFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:BFP,GSM3912418,GSM3912418: CoBFP209; Danio rerio; RNA Seq,GSM3912418,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912418,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1209.fastq.gz,fastq,1253360625.0,16711475.0,GSM3912418 r1,0:75 1:0,A:318671940;C:312437086;G:310765707;T:311436404;N:49488,75,0,,,318671940,312437086,310765707,311436404,49488,SRX6385167,SRS5044685,SRA915985,GEO,University of Bern,1,0.91327,,0.10449,,0.84455,,0.52145,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52987,SRR9622322,SRX6385166,SRS5044683,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,CICh195,GSM3912417,,source name:Adult zebrafish heart Cryoinjury RFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,CICh195,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Cryoinjury RFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,GSM3912417,GSM3912417: CICh195; Danio rerio; RNA Seq,GSM3912417,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912417,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1195.fastq.gz,fastq,760336200.0,10137816.0,GSM3912417 r1,0:75 1:0,A:197955217;C:186699045;G:188337634;T:187315707;N:28597,75,0,,,197955217,186699045,188337634,187315707,28597,SRX6385166,SRS5044683,SRA915985,GEO,University of Bern,1,0.86445,,0.10729,,0.80693,,0.50372,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52988,SRR9622321,SRX6385165,SRS5044684,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,CICh193,GSM3912416,,source name:Adult zebrafish heart Cryoinjury RFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,CICh193,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Cryoinjury RFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,GSM3912416,GSM3912416: CICh193; Danio rerio; RNA Seq,GSM3912416,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912416,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1193.fastq.gz,fastq,1051943325.0,14025911.0,GSM3912416 r1,0:75 1:0,A:259094262;C:271341984;G:266737236;T:254728997;N:40846,75,0,,,259094262,271341984,266737236,254728997,40846,SRX6385165,SRS5044684,SRA915985,GEO,University of Bern,1,0.90754,,0.14162,,0.82747,,0.56046,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52989,SRR9622320,SRX6385164,SRS5044682,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,CICh192,GSM3912415,,source name:Adult zebrafish heart Cryoinjury RFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,CICh192,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Cryoinjury RFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,GSM3912415,GSM3912415: CICh192; Danio rerio; RNA Seq,GSM3912415,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912415,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1192.fastq.gz,fastq,954536625.0,12727155.0,GSM3912415 r1,0:75 1:0,A:246047509;C:238498846;G:234882224;T:235070042;N:38004,75,0,,,246047509,238498846,234882224,235070042,38004,SRX6385164,SRS5044682,SRA915985,GEO,University of Bern,1,0.83549,,0.08499,,0.84451,,0.58547,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52990,SRR9622319,SRX6385163,SRS5044681,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,CICh191,GSM3912414,,source name:Adult zebrafish heart Cryoinjury RFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,CICh191,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Cryoinjury RFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,GSM3912414,GSM3912414: CICh191; Danio rerio; RNA Seq,GSM3912414,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912414,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1191.fastq.gz,fastq,874685850.0,11662478.0,GSM3912414 r1,0:75 1:0,A:231961841;C:213407487;G:211293702;T:217989158;N:33662,75,0,,,231961841,213407487,211293702,217989158,33662,SRX6385163,SRS5044681,SRA915985,GEO,University of Bern,1,0.81595,,0.0379,,0.9203,,0.59806,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52991,SRR9622318,SRX6385162,SRS5044680,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,CIMBFP190,GSM3912413,,source name:Adult zebrafish heart Cryoinjury BFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:BFP,CIMBFP190,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Cryoinjury BFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:BFP,GSM3912413,GSM3912413: CIMBFP190; Danio rerio; RNA Seq,GSM3912413,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912413,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1190.fastq.gz,fastq,845036400.0,11267152.0,GSM3912413 r1,0:75 1:0,A:217443971;C:211448387;G:210065469;T:206046308;N:32265,75,0,,,217443971,211448387,210065469,206046308,32265,SRX6385162,SRS5044680,SRA915985,GEO,University of Bern,1,0.79896,,0.05748,,0.85583,,0.54055,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52992,SRR9622317,SRX6385161,SRS5044679,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,CICh189,GSM3912412,,source name:Adult zebrafish heart Cryoinjury RFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,CICh189,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Cryoinjury RFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,GSM3912412,GSM3912412: CICh189; Danio rerio; RNA Seq,GSM3912412,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912412,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1189.fastq.gz,fastq,1013609175.0,13514789.0,GSM3912412 r1,0:75 1:0,A:262876076;C:250736244;G:250695869;T:249263383;N:37603,75,0,,,262876076,250736244,250695869,249263383,37603,SRX6385161,SRS5044679,SRA915985,GEO,University of Bern,1,0.78917,,0.10477,,0.85348,,0.56355,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52993,SRR9622316,SRX6385160,SRS5044678,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,CICh177,GSM3912411,,source name:Adult zebrafish heart Cryoinjury RFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,CICh177,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Cryoinjury RFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,GSM3912411,GSM3912411: CICh177; Danio rerio; RNA Seq,GSM3912411,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912411,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1177.fastq.gz,fastq,1000978575.0,13346381.0,GSM3912411 r1,0:75 1:0,A:255327494;C:253513930;G:252985056;T:239112717;N:39378,75,0,,,255327494,253513930,252985056,239112717,39378,SRX6385160,SRS5044678,SRA915985,GEO,University of Bern,1,0.80529,,0.09832,,0.85271,,0.57581,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52994,SRR9622315,SRX6385159,SRS5044677,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,CICh169,GSM3912410,,source name:Adult zebrafish heart Cryoinjury RFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,CICh169,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Cryoinjury RFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,GSM3912410,GSM3912410: CICh169; Danio rerio; RNA Seq,GSM3912410,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912410,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1169.fastq.gz,fastq,941390175.0,12551869.0,GSM3912410 r1,0:75 1:0,A:234681331;C:242089137;G:237049068;T:227533115;N:37524,75,0,,,234681331,242089137,237049068,227533115,37524,SRX6385159,SRS5044677,SRA915985,GEO,University of Bern,1,0.87263,,0.05965,,0.93219,,0.50852,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52995,SRR9622314,SRX6385158,SRS5044676,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,CIMBFP73,GSM3912409,,source name:Adult zebrafish heart Cryoinjury BFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:BFP,CIMBFP73,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Cryoinjury BFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:BFP,GSM3912409,GSM3912409: CIMBFP73; Danio rerio; RNA Seq,GSM3912409,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912409,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane173.fastq.gz,fastq,1067202675.0,14229369.0,GSM3912409 r1,0:75 1:0,A:274385908;C:267209053;G:260901436;T:264665252;N:41026,75,0,,,274385908,267209053,260901436,264665252,41026,SRX6385158,SRS5044676,SRA915985,GEO,University of Bern,1,0.91399,,0.06339,,0.87097,,0.61623,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52996,SRR9622313,SRX6385157,SRS5044675,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,CICh49,GSM3912408,,source name:Adult zebrafish heart Cryoinjury RFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,CICh49,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Cryoinjury RFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,GSM3912408,GSM3912408: CICh49; Danio rerio; RNA Seq,GSM3912408,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912408,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane149.fastq.gz,fastq,1242563700.0,16567516.0,GSM3912408 r1,0:75 1:0,A:317197808;C:309171653;G:304904926;T:311240495;N:48818,75,0,,,317197808,309171653,304904926,311240495,48818,SRX6385157,SRS5044675,SRA915985,GEO,University of Bern,1,0.93499,,0.07754,,0.81611,,0.53072,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52997,SRR9622312,SRX6385156,SRS5044673,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,CIMBFP41,GSM3912407,,source name:Adult zebrafish heart Cryoinjury BFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:BFP,CIMBFP41,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Cryoinjury BFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:BFP,GSM3912407,GSM3912407: CIMBFP41; Danio rerio; RNA Seq,GSM3912407,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912407,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane141.fastq.gz,fastq,1032399900.0,13765332.0,GSM3912407 r1,0:75 1:0,A:259362454;C:261716590;G:257581610;T:253699193;N:40053,75,0,,,259362454,261716590,257581610,253699193,40053,SRX6385156,SRS5044673,SRA915985,GEO,University of Bern,1,0.93398,,0.08146,,0.80633,,0.53714,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52998,SRR9622311,SRX6385155,SRS5044671,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,CICh33,GSM3912406,,source name:Adult zebrafish heart Cryoinjury RFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,CICh33,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Cryoinjury RFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,GSM3912406,GSM3912406: CICh33; Danio rerio; RNA Seq,GSM3912406,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912406,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane133.fastq.gz,fastq,1224081525.0,16321087.0,GSM3912406 r1,0:75 1:0,A:315927881;C:302212373;G:297619927;T:308272023;N:49321,75,0,,,315927881,302212373,297619927,308272023,49321,SRX6385155,SRS5044671,SRA915985,GEO,University of Bern,1,0.92945,,0.05906,,0.8354,,0.53423,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 52999,SRR9622310,SRX6385154,SRS5044674,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,CICh17,GSM3912405,,source name:Adult zebrafish heart Cryoinjury RFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,CICh17,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Cryoinjury RFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,GSM3912405,GSM3912405: CICh17; Danio rerio; RNA Seq,GSM3912405,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912405,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane117.fastq.gz,fastq,1274673675.0,16995649.0,GSM3912405 r1,0:75 1:0,A:330587931;C:314640268;G:311295261;T:318100468;N:49747,75,0,,,330587931,314640268,311295261,318100468,49747,SRX6385154,SRS5044674,SRA915985,GEO,University of Bern,1,0.91296,,0.032,,0.87657,,0.50975,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 53000,SRR9622309,SRX6385153,SRS5044672,SRP212668,PRJNA551951,Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish ,GSE133571,Transcriptome Analysis,During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation,,pubmed:31644901,,CICh1,GSM3912404,,source name:Adult zebrafish heart Cryoinjury RFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,CICh1,FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts,Adult zebrafish heart Cryoinjury RFP,,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,,strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Cryoinjury|tissue:Adult zebrafish heart|sorted cell population:RFP,GSM3912404,GSM3912404: CICh1; Danio rerio; RNA Seq,GSM3912404,,1,0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 ,GEO Accession:GSM3912404,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP212668,,,HVJ22BGX5_sox10_18s002081-1-1_Sande_lane11.fastq.gz,fastq,1166281575.0,15550421.0,GSM3912404 r1,0:75 1:0,A:304544426;C:284421666;G:282271207;T:294998918;N:45358,75,0,,,304544426,284421666,282271207,294998918,45358,SRX6385153,SRS5044672,SRA915985,GEO,University of Bern,1,0.91624,,0.04725,,0.87858,,0.54636,,75,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Switzerland,2019-07-01,Adult,Adult,Heart,Cardiovascular System 60871,SRR12610271,SRX9093637,SRS7339297,SRP281427,PRJNA662347,Cardiomyocyte heterogeneity in zebrafish development and regeneration,GSE157662,Transcriptome Analysis,Contrary to adult mammals zebrafish are able to regenerate their heart post cardiac injury. This regenerative response relies in part on the endogenous ability of cardiomyocytes CMs to dedifferentiate and proliferate to replenish the lost muscle. However CM heterogeneity and population dynamics during development and regeneration remain poorly understood. Through comparative transcriptomic analyses of the developing and adult zebrafish heart we identified tnnc2 and tnni4b.3 expression as markers for CMs at early and late developmental stages respectively. Using newly developed reporter lines for these genes we investigated their expression dynamics during development and regeneration and observed interesting expression patterns. tnnc2 reporter lines label most CMs at embryonic stages and this labeling declines rapidly during larval stages; in adult hearts expression is only detectable in a subset of CMs. Conversely expression of a tnni4b.3 reporter is initially visible in outer curvature CMs at larval stages and it is subsequently present in a vast majority of the CMs in adult hearts. Interestingly we find that the adult CMs labeled by the embryonic reporter display higher levels of Tgtp1:EGFP expression which indicates active Notch signaling. To further characterize this CM population we performed transcriptomic analysis and found that it expresses genes encoding components of the Notch signaling pathway as well as markers of immature CMs. Moreover during heart regeneration proliferating CMs in the injured area activate the embryonic CM reporter. Overall our findings provide further evidence of cardiomyocyte heterogeneity in the adult zebrafish heart. Overall design: Total RNA was isolated from sorted myl7:EGFP+ 7000 cells and tp1:EGFP+/myl7:DsRed2 NLS+ 2000 cells. In both cases RNA was extracted using RNeasy Micro Kit Qiagen following manufacturer's instructions.,,pubmed:33857482,,tp1 2,GSM4772983,,source name:FACS sorted tp1:EGFP+/myl7:DsRed2 NLS+ zebrafish cardiomyocytes|developmental stage:Adult|cell type:Cardiomyocytes|tissue:Heart|genotype:tp1:EGFP+/myl7:DsRed2 NLS+,tp1 2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Bolger et al. 2014. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11.98 using STAR 2.6.1d with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. 2013. The number of reads aligning to genes was counted with FeatureCounts tool from the Subread package 1.6.5 Liao et al. 2014. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Differentially expressed genes were identified using DESeq2 version 1.26.0 Love et al. 2014. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanRer11 Supplementary files format and content: counts.matrix.norm anno,FACS sorted tp1:EGFP+/myl7:DsRed2 NLS+ zebrafish cardiomyocytes,,For RNA seq RNA was isolated from sorted myl7:EGFP+ and tp1:EGFP+/myl7:DsRed2 NLS+ ventricular zebrafish CMs using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and approximately 1 2ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech and NEXTflexTM Rapid Directional qRNA Seq Kit Bioo Scientific following manufacturers protocol.,,developmental stage:Adult|cell type:Cardiomyocytes|tissue:Heart|genotype:tp1:EGFP+/myl7:DsRed2 NLS+,GSM4772983,GSM4772983: tp1 2; Danio rerio; RNA Seq,GSM4772983,,1,For RNA seq RNA was isolated from sorted myl7:EGFP+ and tp1:EGFP+/myl7:DsRed2 NLS+ ventricular zebrafish CMs using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and approximately 1 2ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech and NEXTflexTM Rapid Directional qRNA Seq Kit Bioo Scientific following manufacturers protocol.,GEO Accession:GSM4772983,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP281427,,,Ruben_sample_tp1_2_R1.fastq.gz,fastq,1707731673.0,22930695.0,GSM4772983 r1,0:74.47 1:0,A:483180233;C:348675452;G:356254603;T:519590347;N:31038,74,0,,,483180233,348675452,356254603,519590347,31038,SRX9093637,SRS7339297,SRA1122721,GEO,MPI for heart and lung research,1,0.80112,,0.13321,,0.85303,,0.46314,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2020-09-08,Adult,Adult,Heart,Cardiovascular System 60872,SRR12610270,SRX9093636,SRS7339296,SRP281427,PRJNA662347,Cardiomyocyte heterogeneity in zebrafish development and regeneration,GSE157662,Transcriptome Analysis,Contrary to adult mammals zebrafish are able to regenerate their heart post cardiac injury. This regenerative response relies in part on the endogenous ability of cardiomyocytes CMs to dedifferentiate and proliferate to replenish the lost muscle. However CM heterogeneity and population dynamics during development and regeneration remain poorly understood. Through comparative transcriptomic analyses of the developing and adult zebrafish heart we identified tnnc2 and tnni4b.3 expression as markers for CMs at early and late developmental stages respectively. Using newly developed reporter lines for these genes we investigated their expression dynamics during development and regeneration and observed interesting expression patterns. tnnc2 reporter lines label most CMs at embryonic stages and this labeling declines rapidly during larval stages; in adult hearts expression is only detectable in a subset of CMs. Conversely expression of a tnni4b.3 reporter is initially visible in outer curvature CMs at larval stages and it is subsequently present in a vast majority of the CMs in adult hearts. Interestingly we find that the adult CMs labeled by the embryonic reporter display higher levels of Tgtp1:EGFP expression which indicates active Notch signaling. To further characterize this CM population we performed transcriptomic analysis and found that it expresses genes encoding components of the Notch signaling pathway as well as markers of immature CMs. Moreover during heart regeneration proliferating CMs in the injured area activate the embryonic CM reporter. Overall our findings provide further evidence of cardiomyocyte heterogeneity in the adult zebrafish heart. Overall design: Total RNA was isolated from sorted myl7:EGFP+ 7000 cells and tp1:EGFP+/myl7:DsRed2 NLS+ 2000 cells. In both cases RNA was extracted using RNeasy Micro Kit Qiagen following manufacturer's instructions.,,pubmed:33857482,,tp1 1,GSM4772982,,source name:FACS sorted tp1:EGFP+/myl7:DsRed2 NLS+ zebrafish cardiomyocytes|developmental stage:Adult|cell type:Cardiomyocytes|tissue:Heart|genotype:tp1:EGFP+/myl7:DsRed2 NLS+,tp1 1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Bolger et al. 2014. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11.98 using STAR 2.6.1d with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. 2013. The number of reads aligning to genes was counted with FeatureCounts tool from the Subread package 1.6.5 Liao et al. 2014. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Differentially expressed genes were identified using DESeq2 version 1.26.0 Love et al. 2014. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanRer11 Supplementary files format and content: counts.matrix.norm anno,FACS sorted tp1:EGFP+/myl7:DsRed2 NLS+ zebrafish cardiomyocytes,,For RNA seq RNA was isolated from sorted myl7:EGFP+ and tp1:EGFP+/myl7:DsRed2 NLS+ ventricular zebrafish CMs using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and approximately 1 2ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech and NEXTflexTM Rapid Directional qRNA Seq Kit Bioo Scientific following manufacturers protocol.,,developmental stage:Adult|cell type:Cardiomyocytes|tissue:Heart|genotype:tp1:EGFP+/myl7:DsRed2 NLS+,GSM4772982,GSM4772982: tp1 1; Danio rerio; RNA Seq,GSM4772982,,1,For RNA seq RNA was isolated from sorted myl7:EGFP+ and tp1:EGFP+/myl7:DsRed2 NLS+ ventricular zebrafish CMs using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and approximately 1 2ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech and NEXTflexTM Rapid Directional qRNA Seq Kit Bioo Scientific following manufacturers protocol.,GEO Accession:GSM4772982,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP281427,,,Ruben_sample_tp1_1_R1.fastq.gz,fastq,1720450200.0,22939336.0,GSM4772982 r1,0:75 1:0,A:497019985;C:361171515;G:363825078;T:497852941;N:580681,75,0,,,497019985,361171515,363825078,497852941,580681,SRX9093636,SRS7339296,SRA1122721,GEO,MPI for heart and lung research,1,0.91207,,0.14937,,0.83806,,0.43897,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2020-09-08,Adult,Adult,Heart,Cardiovascular System 60873,SRR12610269,SRX9093635,SRS7339295,SRP281427,PRJNA662347,Cardiomyocyte heterogeneity in zebrafish development and regeneration,GSE157662,Transcriptome Analysis,Contrary to adult mammals zebrafish are able to regenerate their heart post cardiac injury. This regenerative response relies in part on the endogenous ability of cardiomyocytes CMs to dedifferentiate and proliferate to replenish the lost muscle. However CM heterogeneity and population dynamics during development and regeneration remain poorly understood. Through comparative transcriptomic analyses of the developing and adult zebrafish heart we identified tnnc2 and tnni4b.3 expression as markers for CMs at early and late developmental stages respectively. Using newly developed reporter lines for these genes we investigated their expression dynamics during development and regeneration and observed interesting expression patterns. tnnc2 reporter lines label most CMs at embryonic stages and this labeling declines rapidly during larval stages; in adult hearts expression is only detectable in a subset of CMs. Conversely expression of a tnni4b.3 reporter is initially visible in outer curvature CMs at larval stages and it is subsequently present in a vast majority of the CMs in adult hearts. Interestingly we find that the adult CMs labeled by the embryonic reporter display higher levels of Tgtp1:EGFP expression which indicates active Notch signaling. To further characterize this CM population we performed transcriptomic analysis and found that it expresses genes encoding components of the Notch signaling pathway as well as markers of immature CMs. Moreover during heart regeneration proliferating CMs in the injured area activate the embryonic CM reporter. Overall our findings provide further evidence of cardiomyocyte heterogeneity in the adult zebrafish heart. Overall design: Total RNA was isolated from sorted myl7:EGFP+ 7000 cells and tp1:EGFP+/myl7:DsRed2 NLS+ 2000 cells. In both cases RNA was extracted using RNeasy Micro Kit Qiagen following manufacturer's instructions.,,pubmed:33857482,,myl7 2,GSM4772981,,source name:FACS sorted myl7:EGFP+ zebrafish cardiomyocytes|developmental stage:Adult|cell type:Cardiomyocytes|tissue:Heart|genotype:myl7:EGFP+,myl7 2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Bolger et al. 2014. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11.98 using STAR 2.6.1d with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. 2013. The number of reads aligning to genes was counted with FeatureCounts tool from the Subread package 1.6.5 Liao et al. 2014. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Differentially expressed genes were identified using DESeq2 version 1.26.0 Love et al. 2014. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanRer11 Supplementary files format and content: counts.matrix.norm anno,FACS sorted myl7:EGFP+ zebrafish cardiomyocytes,,For RNA seq RNA was isolated from sorted myl7:EGFP+ and tp1:EGFP+/myl7:DsRed2 NLS+ ventricular zebrafish CMs using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and approximately 1 2ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech and NEXTflexTM Rapid Directional qRNA Seq Kit Bioo Scientific following manufacturers protocol.,,developmental stage:Adult|cell type:Cardiomyocytes|tissue:Heart|genotype:myl7:EGFP+,GSM4772981,GSM4772981: myl7 2; Danio rerio; RNA Seq,GSM4772981,,1,For RNA seq RNA was isolated from sorted myl7:EGFP+ and tp1:EGFP+/myl7:DsRed2 NLS+ ventricular zebrafish CMs using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and approximately 1 2ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech and NEXTflexTM Rapid Directional qRNA Seq Kit Bioo Scientific following manufacturers protocol.,GEO Accession:GSM4772981,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP281427,,,Ruben_sample_myl7_2_R1.fastq.gz,fastq,2216173397.0,29748630.0,GSM4772981 r1,0:74.50 1:0,A:616722527;C:458360132;G:466793177;T:674039912;N:257649,74,0,,,616722527,458360132,466793177,674039912,257649,SRX9093635,SRS7339295,SRA1122721,GEO,MPI for heart and lung research,1,0.8122,,0.13579,,0.86419,,0.42953,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2020-09-08,Adult,Adult,Heart,Cardiovascular System 60874,SRR12610268,SRX9093634,SRS7339294,SRP281427,PRJNA662347,Cardiomyocyte heterogeneity in zebrafish development and regeneration,GSE157662,Transcriptome Analysis,Contrary to adult mammals zebrafish are able to regenerate their heart post cardiac injury. This regenerative response relies in part on the endogenous ability of cardiomyocytes CMs to dedifferentiate and proliferate to replenish the lost muscle. However CM heterogeneity and population dynamics during development and regeneration remain poorly understood. Through comparative transcriptomic analyses of the developing and adult zebrafish heart we identified tnnc2 and tnni4b.3 expression as markers for CMs at early and late developmental stages respectively. Using newly developed reporter lines for these genes we investigated their expression dynamics during development and regeneration and observed interesting expression patterns. tnnc2 reporter lines label most CMs at embryonic stages and this labeling declines rapidly during larval stages; in adult hearts expression is only detectable in a subset of CMs. Conversely expression of a tnni4b.3 reporter is initially visible in outer curvature CMs at larval stages and it is subsequently present in a vast majority of the CMs in adult hearts. Interestingly we find that the adult CMs labeled by the embryonic reporter display higher levels of Tgtp1:EGFP expression which indicates active Notch signaling. To further characterize this CM population we performed transcriptomic analysis and found that it expresses genes encoding components of the Notch signaling pathway as well as markers of immature CMs. Moreover during heart regeneration proliferating CMs in the injured area activate the embryonic CM reporter. Overall our findings provide further evidence of cardiomyocyte heterogeneity in the adult zebrafish heart. Overall design: Total RNA was isolated from sorted myl7:EGFP+ 7000 cells and tp1:EGFP+/myl7:DsRed2 NLS+ 2000 cells. In both cases RNA was extracted using RNeasy Micro Kit Qiagen following manufacturer's instructions.,,pubmed:33857482,,myl7 1,GSM4772980,,source name:FACS sorted myl7:EGFP+ zebrafish cardiomyocytes|developmental stage:Adult|cell type:Cardiomyocytes|tissue:Heart|genotype:myl7:EGFP+,myl7 1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Bolger et al. 2014. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11.98 using STAR 2.6.1d with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. 2013. The number of reads aligning to genes was counted with FeatureCounts tool from the Subread package 1.6.5 Liao et al. 2014. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Differentially expressed genes were identified using DESeq2 version 1.26.0 Love et al. 2014. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanRer11 Supplementary files format and content: counts.matrix.norm anno,FACS sorted myl7:EGFP+ zebrafish cardiomyocytes,,For RNA seq RNA was isolated from sorted myl7:EGFP+ and tp1:EGFP+/myl7:DsRed2 NLS+ ventricular zebrafish CMs using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and approximately 1 2ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech and NEXTflexTM Rapid Directional qRNA Seq Kit Bioo Scientific following manufacturers protocol.,,developmental stage:Adult|cell type:Cardiomyocytes|tissue:Heart|genotype:myl7:EGFP+,GSM4772980,GSM4772980: myl7 1; Danio rerio; RNA Seq,GSM4772980,,1,For RNA seq RNA was isolated from sorted myl7:EGFP+ and tp1:EGFP+/myl7:DsRed2 NLS+ ventricular zebrafish CMs using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and approximately 1 2ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech and NEXTflexTM Rapid Directional qRNA Seq Kit Bioo Scientific following manufacturers protocol.,GEO Accession:GSM4772980,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP281427,,,Ruben_sample_myl7_1_R1.fastq.gz,fastq,2949217134.0,39569236.0,GSM4772980 r1,0:74.53 1:0,A:846793773;C:636612082;G:642754162;T:823002049;N:55068,74,0,,,846793773,636612082,642754162,823002049,55068,SRX9093634,SRS7339294,SRA1122721,GEO,MPI for heart and lung research,1,0.92424,,0.13815,,0.84524,,0.47678,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2020-09-08,Adult,Adult,Heart,Cardiovascular System 62466,SRR13191910,SRX9626278,SRS7827449,SRP295659,PRJNA682370,Identification of Snai1b targets in zebrafish heart by transcriptomic analysis,GSE162604,Transcriptome Analysis,Purpose: identifying with RNA seq genes targets of Snai1b during zebrafish cardiac development. Results: we identified several differential expressed genes in particular cytoskeletal genes. In particular the intermediate filament gene desmin b is upregulated. Overall design: Hearts were manually dissected at 48 hpf from snai1b mutants and wild type,,pubmed:34152269,,Hearts homo 2,GSM4955126,,source name:Heart|developmental stage:48 hpf|tissue:Heart|genotype:snai1b / ,Hearts homo 2,The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.39 was used to trim reads with a quality drop below a mean of Q20 in a window of 10 nucleotides . Only reads between 30 and 150 nucleotides were used in subsequent analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11.92 using STAR 2.6.1d with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package Liao et al. 2014. Only reads mapping at least partially inside exons were admitted and aggregated per gene while reads overlapping multiple genes or aligning to multiple regions were excluded from further analyses. Differentially expressed genes were identified using DESeq2 version 1.18.1. The Ensembl annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Genome build: DanRer11 Supplementary files format and content: library size normalized counts,Heart,,48 hpf Tgmyl7:BFP CAAX snai1b+/+ and snai1b / hearts were manually dissected using forceps. Approximately 20 hearts per replicate were pooled and total RNA was isolated using the miRNeasy micro kit combined with on column DNase digestion. Approximately 10 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip GX Touch 24 and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,,developmental stage:48 hpf|tissue:Heart|genotype:snai1b / ,GSM4955126,GSM4955126: Hearts homo 2; Danio rerio; RNA Seq,GSM4955126,,1,48 hpf Tgmyl7:BFP CAAX snai1b+/+ and snai1b / hearts were manually dissected using forceps. Approximately 20 hearts per replicate were pooled and total RNA was isolated using the miRNeasy micro kit combined with on column DNase digestion. Approximately 10 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip GX Touch 24 and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,GEO Accession:GSM4955126,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP295659,,,Felix_AG_4_R1.fastq.gz,fastq,2271568738.0,31924930.0,GSM4955126 r1,0:71.15 1:0,A:634307853;C:505275217;G:504394841;T:627581585;N:9242,71,0,,,634307853,505275217,504394841,627581585,9242,SRX9626278,SRS7827449,SRA1166534,GEO,MPI for heart and lung research,1,0.92646,,0.10199,,0.73109,,0.44675,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2020-12-03,Hatching,Embryo,Heart,Cardiovascular System 62467,SRR13191909,SRX9626277,SRS7827448,SRP295659,PRJNA682370,Identification of Snai1b targets in zebrafish heart by transcriptomic analysis,GSE162604,Transcriptome Analysis,Purpose: identifying with RNA seq genes targets of Snai1b during zebrafish cardiac development. Results: we identified several differential expressed genes in particular cytoskeletal genes. In particular the intermediate filament gene desmin b is upregulated. Overall design: Hearts were manually dissected at 48 hpf from snai1b mutants and wild type,,pubmed:34152269,,Hearts wt 2,GSM4955125,,source name:Heart|developmental stage:48 hpf|tissue:Heart|genotype:wild type,Hearts wt 2,The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.39 was used to trim reads with a quality drop below a mean of Q20 in a window of 10 nucleotides . Only reads between 30 and 150 nucleotides were used in subsequent analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11.92 using STAR 2.6.1d with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package Liao et al. 2014. Only reads mapping at least partially inside exons were admitted and aggregated per gene while reads overlapping multiple genes or aligning to multiple regions were excluded from further analyses. Differentially expressed genes were identified using DESeq2 version 1.18.1. The Ensembl annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Genome build: DanRer11 Supplementary files format and content: library size normalized counts,Heart,,48 hpf Tgmyl7:BFP CAAX snai1b+/+ and snai1b / hearts were manually dissected using forceps. Approximately 20 hearts per replicate were pooled and total RNA was isolated using the miRNeasy micro kit combined with on column DNase digestion. Approximately 10 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip GX Touch 24 and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,,developmental stage:48 hpf|tissue:Heart|genotype:wild type,GSM4955125,GSM4955125: Hearts wt 2; Danio rerio; RNA Seq,GSM4955125,,1,48 hpf Tgmyl7:BFP CAAX snai1b+/+ and snai1b / hearts were manually dissected using forceps. Approximately 20 hearts per replicate were pooled and total RNA was isolated using the miRNeasy micro kit combined with on column DNase digestion. Approximately 10 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip GX Touch 24 and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,GEO Accession:GSM4955125,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP295659,,,Felix_AG_3_R1.fastq.gz,fastq,2312289944.0,32497996.0,GSM4955125 r1,0:71.15 1:0,A:646717753;C:512859953;G:511898920;T:640804094;N:9224,71,0,,,646717753,512859953,511898920,640804094,9224,SRX9626277,SRS7827448,SRA1166534,GEO,MPI for heart and lung research,1,0.93649,,0.1068,,0.72914,,0.44928,,74,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2020-12-03,Hatching,Embryo,Heart,Cardiovascular System 62468,SRR13191908,SRX9626276,SRS7827447,SRP295659,PRJNA682370,Identification of Snai1b targets in zebrafish heart by transcriptomic analysis,GSE162604,Transcriptome Analysis,Purpose: identifying with RNA seq genes targets of Snai1b during zebrafish cardiac development. Results: we identified several differential expressed genes in particular cytoskeletal genes. In particular the intermediate filament gene desmin b is upregulated. Overall design: Hearts were manually dissected at 48 hpf from snai1b mutants and wild type,,pubmed:34152269,,Hearts homo 1,GSM4955124,,source name:Heart|developmental stage:48 hpf|tissue:Heart|genotype:snai1b / ,Hearts homo 1,The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.39 was used to trim reads with a quality drop below a mean of Q20 in a window of 10 nucleotides . Only reads between 30 and 150 nucleotides were used in subsequent analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11.92 using STAR 2.6.1d with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package Liao et al. 2014. Only reads mapping at least partially inside exons were admitted and aggregated per gene while reads overlapping multiple genes or aligning to multiple regions were excluded from further analyses. Differentially expressed genes were identified using DESeq2 version 1.18.1. The Ensembl annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Genome build: DanRer11 Supplementary files format and content: library size normalized counts,Heart,,48 hpf Tgmyl7:BFP CAAX snai1b+/+ and snai1b / hearts were manually dissected using forceps. Approximately 20 hearts per replicate were pooled and total RNA was isolated using the miRNeasy micro kit combined with on column DNase digestion. Approximately 10 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip GX Touch 24 and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,,developmental stage:48 hpf|tissue:Heart|genotype:snai1b / ,GSM4955124,GSM4955124: Hearts homo 1; Danio rerio; RNA Seq,GSM4955124,,1,48 hpf Tgmyl7:BFP CAAX snai1b+/+ and snai1b / hearts were manually dissected using forceps. Approximately 20 hearts per replicate were pooled and total RNA was isolated using the miRNeasy micro kit combined with on column DNase digestion. Approximately 10 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip GX Touch 24 and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,GEO Accession:GSM4955124,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP295659,,,Felix_AG_2_R1.fastq.gz,fastq,2020041285.0,29103593.0,GSM4955124 r1,0:69.41 1:0,A:567463762;C:445189803;G:445150753;T:562228557;N:8410,69,0,,,567463762,445189803,445150753,562228557,8410,SRX9626276,SRS7827447,SRA1166534,GEO,MPI for heart and lung research,1,0.69413,,0.08493,,0.74856,,0.46898,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2020-12-03,Hatching,Embryo,Heart,Cardiovascular System 62469,SRR13191907,SRX9626275,SRS7827446,SRP295659,PRJNA682370,Identification of Snai1b targets in zebrafish heart by transcriptomic analysis,GSE162604,Transcriptome Analysis,Purpose: identifying with RNA seq genes targets of Snai1b during zebrafish cardiac development. Results: we identified several differential expressed genes in particular cytoskeletal genes. In particular the intermediate filament gene desmin b is upregulated. Overall design: Hearts were manually dissected at 48 hpf from snai1b mutants and wild type,,pubmed:34152269,,Hearts wt 1,GSM4955123,,source name:Heart|developmental stage:48 hpf|tissue:Heart|genotype:wild type,Hearts wt 1,The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.39 was used to trim reads with a quality drop below a mean of Q20 in a window of 10 nucleotides . Only reads between 30 and 150 nucleotides were used in subsequent analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11.92 using STAR 2.6.1d with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package Liao et al. 2014. Only reads mapping at least partially inside exons were admitted and aggregated per gene while reads overlapping multiple genes or aligning to multiple regions were excluded from further analyses. Differentially expressed genes were identified using DESeq2 version 1.18.1. The Ensembl annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Genome build: DanRer11 Supplementary files format and content: library size normalized counts,Heart,,48 hpf Tgmyl7:BFP CAAX snai1b+/+ and snai1b / hearts were manually dissected using forceps. Approximately 20 hearts per replicate were pooled and total RNA was isolated using the miRNeasy micro kit combined with on column DNase digestion. Approximately 10 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip GX Touch 24 and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,,developmental stage:48 hpf|tissue:Heart|genotype:wild type,GSM4955123,GSM4955123: Hearts wt 1; Danio rerio; RNA Seq,GSM4955123,,1,48 hpf Tgmyl7:BFP CAAX snai1b+/+ and snai1b / hearts were manually dissected using forceps. Approximately 20 hearts per replicate were pooled and total RNA was isolated using the miRNeasy micro kit combined with on column DNase digestion. Approximately 10 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip GX Touch 24 and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,GEO Accession:GSM4955123,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP295659,,,Felix_AG_1_R1.fastq.gz,fastq,1703811137.0,24973727.0,GSM4955123 r1,0:68.22 1:0,A:492162789;C:362546969;G:362688130;T:486406049;N:7200,68,0,,,492162789,362546969,362688130,486406049,7200,SRX9626275,SRS7827446,SRA1166534,GEO,MPI for heart and lung research,1,0.57659,,0.0674,,0.77327,,0.47468,,72,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2020-12-03,Hatching,Embryo,Heart,Cardiovascular System 64340,SRR14559684,SRX10902998,SRS8995273,SRP319994,PRJNA730305,Identification of Tcf21 downstream genes in the epicardial cells and cardiomyocytes by transcriptomic analysis,GSE174505,Transcriptome Analysis,Purpose: Studying the epicardium myocardium crosstalk in the zebrafish larval heart. To do so we aimed to identify with RNA seq the genes dysregulated following the loss of the epicardial marker gene tcf21 in sorted epicardial cells and cardiomyocytes. Results: We first analyzed the transcriptome of epicardial and myocardial WT cells and identified cell type specific/enriched genes. Then we identified several differential expressed genes in tcf21 mutants including several ligand receptor couples known to mediate the epicardium myocardium crosstalk. Overall design: Hearts were manually extracted from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae. Hearts were dissociated into single cell suspensions and FACS was performed to sort epicardial and myocardial cells based on the fluorescence signal.,,pubmed:36172839,,CMs tcf21 / 96 hpf [CM Mut 2],GSM5318588,,tissue:Sorted cardiomyocytes|strain:Tgmyl7:mCherry CAAX+ Tgtcf21:nls.EGFP |genotype:tcf21 / |developmental stage:96 hpf|cell type:Cardiomyocytes,CMs tcf21 / 96 hpf [CM Mut 2],Trimmomatic version 0.39 was used to trim reads with a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were used in subsequent analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 Ensembl release 99 using STAR 2.7.3a with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package Liao et al. 2014. Only reads mapping at least partially inside exons were admitted and aggregated per gene while reads overlapping multiple genes or aligning to multiple regions were excluded from further analyses. Differentially expressed genes were identified using DESeq2 version 1.26.0 Love et al. 2014. To remove a batch effect from the comparison the replicates were presented to DESeq2 as covariates DMSO 1/Inhib 1 = 1 DMSO 2/Inhib 2 = 2. The Ensembl annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers. Genome build: DanRer11 GRCz11 Supplementary files format and content: counts.matrix.norm anno.txt: Tab delimited text file includes library size normalized counts.,Sorted cardiomyocytes,,Hearts from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000 1000 cells per replicate were used and total RNA was isolated using the miRNeasy micro kit Qiagen combined with on column DNase digestion. 4 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,,strain:Tgmyl7:mCherry CAAX+ Tgtcf21:nls.EGFP |genotype:tcf21 / |developmental stage:96 hpf|cell type:Cardiomyocytes,GSM5318588,GSM5318588: CMs tcf21 / 96 hpf [CM Mut 2]; Danio rerio; RNA Seq,GSM5318588,,1,Hearts from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000 1000 cells per replicate were used and total RNA was isolated using the miRNeasy micro kit Qiagen combined with on column DNase digestion. 4 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,GEO Accession:GSM5318588,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP319994,,loader:fastq load.py,Giulia_Lib_CM_Mut_2_R1.fastq.gz,fastq,3564657606.0,48540431.0,GSM5318588 r1,0:73.44,A:999246550;C:794443225;G:807972211;T:962982265;N:13355,73,,,,999246550,794443225,807972211,962982265,13355,SRX10902998,SRS8995273,SRA1232823,GEO,MPI for heart and lung research,1,0.92849,,0.0817,,0.81253,,0.47508,,74,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2021-05-16,Larval,Larval,Heart,Cardiovascular System 64341,SRR14559683,SRX10902997,SRS8995272,SRP319994,PRJNA730305,Identification of Tcf21 downstream genes in the epicardial cells and cardiomyocytes by transcriptomic analysis,GSE174505,Transcriptome Analysis,Purpose: Studying the epicardium myocardium crosstalk in the zebrafish larval heart. To do so we aimed to identify with RNA seq the genes dysregulated following the loss of the epicardial marker gene tcf21 in sorted epicardial cells and cardiomyocytes. Results: We first analyzed the transcriptome of epicardial and myocardial WT cells and identified cell type specific/enriched genes. Then we identified several differential expressed genes in tcf21 mutants including several ligand receptor couples known to mediate the epicardium myocardium crosstalk. Overall design: Hearts were manually extracted from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae. Hearts were dissociated into single cell suspensions and FACS was performed to sort epicardial and myocardial cells based on the fluorescence signal.,,pubmed:36172839,,CMs tcf21 / 96 hpf [CM Mut 1],GSM5318587,,tissue:Sorted cardiomyocytes|strain:Tgmyl7:mCherry CAAX+ Tgtcf21:nls.EGFP |genotype:tcf21 / |developmental stage:96 hpf|cell type:Cardiomyocytes,CMs tcf21 / 96 hpf [CM Mut 1],Trimmomatic version 0.39 was used to trim reads with a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were used in subsequent analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 Ensembl release 99 using STAR 2.7.3a with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package Liao et al. 2014. Only reads mapping at least partially inside exons were admitted and aggregated per gene while reads overlapping multiple genes or aligning to multiple regions were excluded from further analyses. Differentially expressed genes were identified using DESeq2 version 1.26.0 Love et al. 2014. To remove a batch effect from the comparison the replicates were presented to DESeq2 as covariates DMSO 1/Inhib 1 = 1 DMSO 2/Inhib 2 = 2. The Ensembl annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers. Genome build: DanRer11 GRCz11 Supplementary files format and content: counts.matrix.norm anno.txt: Tab delimited text file includes library size normalized counts.,Sorted cardiomyocytes,,Hearts from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000 1000 cells per replicate were used and total RNA was isolated using the miRNeasy micro kit Qiagen combined with on column DNase digestion. 4 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,,strain:Tgmyl7:mCherry CAAX+ Tgtcf21:nls.EGFP |genotype:tcf21 / |developmental stage:96 hpf|cell type:Cardiomyocytes,GSM5318587,GSM5318587: CMs tcf21 / 96 hpf [CM Mut 1]; Danio rerio; RNA Seq,GSM5318587,,1,Hearts from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000 1000 cells per replicate were used and total RNA was isolated using the miRNeasy micro kit Qiagen combined with on column DNase digestion. 4 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,GEO Accession:GSM5318587,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP319994,,loader:fastq load.py,Giulia_Lib_CM_Mut_1_R1.fastq.gz,fastq,3236330818.0,44072575.0,GSM5318587 r1,0:73.43,A:910021876;C:719913281;G:732777305;T:873606347;N:12009,73,,,,910021876,719913281,732777305,873606347,12009,SRX10902997,SRS8995272,SRA1232823,GEO,MPI for heart and lung research,1,0.92826,,0.08295,,0.81578,,0.486,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2021-05-16,Larval,Larval,Heart,Cardiovascular System 64342,SRR14559690,SRX10902996,SRS8995271,SRP319994,PRJNA730305,Identification of Tcf21 downstream genes in the epicardial cells and cardiomyocytes by transcriptomic analysis,GSE174505,Transcriptome Analysis,Purpose: Studying the epicardium myocardium crosstalk in the zebrafish larval heart. To do so we aimed to identify with RNA seq the genes dysregulated following the loss of the epicardial marker gene tcf21 in sorted epicardial cells and cardiomyocytes. Results: We first analyzed the transcriptome of epicardial and myocardial WT cells and identified cell type specific/enriched genes. Then we identified several differential expressed genes in tcf21 mutants including several ligand receptor couples known to mediate the epicardium myocardium crosstalk. Overall design: Hearts were manually extracted from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae. Hearts were dissociated into single cell suspensions and FACS was performed to sort epicardial and myocardial cells based on the fluorescence signal.,,pubmed:36172839,,EpiCs tcf21+/+ 96 hpf [Epi WT 2],GSM5318594,,tissue:Sorted epicardial cells|strain:Tgtcf21:nls EGFP+|genotype:tcf21+/+|developmental stage:96 hpf|cell type:Epicardial cells,EpiCs tcf21+/+ 96 hpf [Epi WT 2],Trimmomatic version 0.39 was used to trim reads with a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were used in subsequent analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 Ensembl release 99 using STAR 2.7.3a with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package Liao et al. 2014. Only reads mapping at least partially inside exons were admitted and aggregated per gene while reads overlapping multiple genes or aligning to multiple regions were excluded from further analyses. Differentially expressed genes were identified using DESeq2 version 1.26.0 Love et al. 2014. To remove a batch effect from the comparison the replicates were presented to DESeq2 as covariates DMSO 1/Inhib 1 = 1 DMSO 2/Inhib 2 = 2. The Ensembl annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers. Genome build: DanRer11 GRCz11 Supplementary files format and content: counts.matrix.norm anno.txt: Tab delimited text file includes library size normalized counts.,Sorted epicardial cells,,Hearts from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000 1000 cells per replicate were used and total RNA was isolated using the miRNeasy micro kit Qiagen combined with on column DNase digestion. 4 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,,strain:Tgtcf21:nls EGFP+|genotype:tcf21+/+|developmental stage:96 hpf|cell type:Epicardial cells,GSM5318594,GSM5318594: EpiCs tcf21+/+ 96 hpf [Epi WT 2]; Danio rerio; RNA Seq,GSM5318594,,1,Hearts from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000 1000 cells per replicate were used and total RNA was isolated using the miRNeasy micro kit Qiagen combined with on column DNase digestion. 4 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,GEO Accession:GSM5318594,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP319994,,loader:fastq load.py,Giulia_Lib_Epi_WT_2_R1.fastq.gz,fastq,3540583732.0,47966008.0,GSM5318594 r1,0:73.81,A:1016068528;C:763620372;G:776940419;T:983941455;N:12958,73,,,,1016068528,763620372,776940419,983941455,12958,SRX10902996,SRS8995271,SRA1232823,GEO,MPI for heart and lung research,1,0.90584,,0.16045,,0.79123,,0.4612,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2021-05-16,Larval,Larval,Heart,Cardiovascular System 64343,SRR14559689,SRX10902995,SRS8995270,SRP319994,PRJNA730305,Identification of Tcf21 downstream genes in the epicardial cells and cardiomyocytes by transcriptomic analysis,GSE174505,Transcriptome Analysis,Purpose: Studying the epicardium myocardium crosstalk in the zebrafish larval heart. To do so we aimed to identify with RNA seq the genes dysregulated following the loss of the epicardial marker gene tcf21 in sorted epicardial cells and cardiomyocytes. Results: We first analyzed the transcriptome of epicardial and myocardial WT cells and identified cell type specific/enriched genes. Then we identified several differential expressed genes in tcf21 mutants including several ligand receptor couples known to mediate the epicardium myocardium crosstalk. Overall design: Hearts were manually extracted from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae. Hearts were dissociated into single cell suspensions and FACS was performed to sort epicardial and myocardial cells based on the fluorescence signal.,,pubmed:36172839,,EpiCs tcf21+/+ 96 hpf [Epi WT 1],GSM5318593,,tissue:Sorted epicardial cells|strain:Tgtcf21:nls EGFP+|genotype:tcf21+/+|developmental stage:96 hpf|cell type:Epicardial cells,EpiCs tcf21+/+ 96 hpf [Epi WT 1],Trimmomatic version 0.39 was used to trim reads with a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were used in subsequent analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 Ensembl release 99 using STAR 2.7.3a with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package Liao et al. 2014. Only reads mapping at least partially inside exons were admitted and aggregated per gene while reads overlapping multiple genes or aligning to multiple regions were excluded from further analyses. Differentially expressed genes were identified using DESeq2 version 1.26.0 Love et al. 2014. To remove a batch effect from the comparison the replicates were presented to DESeq2 as covariates DMSO 1/Inhib 1 = 1 DMSO 2/Inhib 2 = 2. The Ensembl annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers. Genome build: DanRer11 GRCz11 Supplementary files format and content: counts.matrix.norm anno.txt: Tab delimited text file includes library size normalized counts.,Sorted epicardial cells,,Hearts from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000 1000 cells per replicate were used and total RNA was isolated using the miRNeasy micro kit Qiagen combined with on column DNase digestion. 4 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,,strain:Tgtcf21:nls EGFP+|genotype:tcf21+/+|developmental stage:96 hpf|cell type:Epicardial cells,GSM5318593,GSM5318593: EpiCs tcf21+/+ 96 hpf [Epi WT 1]; Danio rerio; RNA Seq,GSM5318593,,1,Hearts from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000 1000 cells per replicate were used and total RNA was isolated using the miRNeasy micro kit Qiagen combined with on column DNase digestion. 4 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,GEO Accession:GSM5318593,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP319994,,loader:fastq load.py,Giulia_Lib_Epi_WT_1_R1.fastq.gz,fastq,3878402012.0,52785328.0,GSM5318593 r1,0:73.48,A:1105990336;C:845212375;G:858550120;T:1068634859;N:14322,73,,,,1105990336,845212375,858550120,1068634859,14322,SRX10902995,SRS8995270,SRA1232823,GEO,MPI for heart and lung research,1,0.90352,,0.16247,,0.78595,,0.46139,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2021-05-16,Larval,Larval,Heart,Cardiovascular System 64344,SRR14559688,SRX10902994,SRS8995269,SRP319994,PRJNA730305,Identification of Tcf21 downstream genes in the epicardial cells and cardiomyocytes by transcriptomic analysis,GSE174505,Transcriptome Analysis,Purpose: Studying the epicardium myocardium crosstalk in the zebrafish larval heart. To do so we aimed to identify with RNA seq the genes dysregulated following the loss of the epicardial marker gene tcf21 in sorted epicardial cells and cardiomyocytes. Results: We first analyzed the transcriptome of epicardial and myocardial WT cells and identified cell type specific/enriched genes. Then we identified several differential expressed genes in tcf21 mutants including several ligand receptor couples known to mediate the epicardium myocardium crosstalk. Overall design: Hearts were manually extracted from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae. Hearts were dissociated into single cell suspensions and FACS was performed to sort epicardial and myocardial cells based on the fluorescence signal.,,pubmed:36172839,,EpiCs tcf21 / 96 hpf [Epi Mut 2],GSM5318592,,tissue:Sorted epicardial cells|strain:Tgtcf21:nls EGFP+|genotype:tcf21 / |developmental stage:96 hpf|cell type:Epicardial cells,EpiCs tcf21 / 96 hpf [Epi Mut 2],Trimmomatic version 0.39 was used to trim reads with a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were used in subsequent analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 Ensembl release 99 using STAR 2.7.3a with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package Liao et al. 2014. Only reads mapping at least partially inside exons were admitted and aggregated per gene while reads overlapping multiple genes or aligning to multiple regions were excluded from further analyses. Differentially expressed genes were identified using DESeq2 version 1.26.0 Love et al. 2014. To remove a batch effect from the comparison the replicates were presented to DESeq2 as covariates DMSO 1/Inhib 1 = 1 DMSO 2/Inhib 2 = 2. The Ensembl annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers. Genome build: DanRer11 GRCz11 Supplementary files format and content: counts.matrix.norm anno.txt: Tab delimited text file includes library size normalized counts.,Sorted epicardial cells,,Hearts from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000 1000 cells per replicate were used and total RNA was isolated using the miRNeasy micro kit Qiagen combined with on column DNase digestion. 4 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,,strain:Tgtcf21:nls EGFP+|genotype:tcf21 / |developmental stage:96 hpf|cell type:Epicardial cells,GSM5318592,GSM5318592: EpiCs tcf21 / 96 hpf [Epi Mut 2]; Danio rerio; RNA Seq,GSM5318592,,1,Hearts from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000 1000 cells per replicate were used and total RNA was isolated using the miRNeasy micro kit Qiagen combined with on column DNase digestion. 4 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,GEO Accession:GSM5318592,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP319994,,loader:fastq load.py,Giulia_Lib_Epi_Mut_2_R1.fastq.gz,fastq,3786135960.0,51574155.0,GSM5318592 r1,0:73.41,A:1073627795;C:831338973;G:843729039;T:1037426163;N:13990,73,,,,1073627795,831338973,843729039,1037426163,13990,SRX10902994,SRS8995269,SRA1232823,GEO,MPI for heart and lung research,1,0.89832,,0.13703,,0.79095,,0.44587,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2021-05-16,Larval,Larval,Heart,Cardiovascular System 64345,SRR14559687,SRX10902993,SRS8995268,SRP319994,PRJNA730305,Identification of Tcf21 downstream genes in the epicardial cells and cardiomyocytes by transcriptomic analysis,GSE174505,Transcriptome Analysis,Purpose: Studying the epicardium myocardium crosstalk in the zebrafish larval heart. To do so we aimed to identify with RNA seq the genes dysregulated following the loss of the epicardial marker gene tcf21 in sorted epicardial cells and cardiomyocytes. Results: We first analyzed the transcriptome of epicardial and myocardial WT cells and identified cell type specific/enriched genes. Then we identified several differential expressed genes in tcf21 mutants including several ligand receptor couples known to mediate the epicardium myocardium crosstalk. Overall design: Hearts were manually extracted from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae. Hearts were dissociated into single cell suspensions and FACS was performed to sort epicardial and myocardial cells based on the fluorescence signal.,,pubmed:36172839,,EpiCs tcf21 / 96 hpf [Epi Mut 1],GSM5318591,,tissue:Sorted epicardial cells|strain:Tgtcf21:nls EGFP+|genotype:tcf21 / |developmental stage:96 hpf|cell type:Epicardial cells,EpiCs tcf21 / 96 hpf [Epi Mut 1],Trimmomatic version 0.39 was used to trim reads with a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were used in subsequent analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 Ensembl release 99 using STAR 2.7.3a with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package Liao et al. 2014. Only reads mapping at least partially inside exons were admitted and aggregated per gene while reads overlapping multiple genes or aligning to multiple regions were excluded from further analyses. Differentially expressed genes were identified using DESeq2 version 1.26.0 Love et al. 2014. To remove a batch effect from the comparison the replicates were presented to DESeq2 as covariates DMSO 1/Inhib 1 = 1 DMSO 2/Inhib 2 = 2. The Ensembl annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers. Genome build: DanRer11 GRCz11 Supplementary files format and content: counts.matrix.norm anno.txt: Tab delimited text file includes library size normalized counts.,Sorted epicardial cells,,Hearts from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000 1000 cells per replicate were used and total RNA was isolated using the miRNeasy micro kit Qiagen combined with on column DNase digestion. 4 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,,strain:Tgtcf21:nls EGFP+|genotype:tcf21 / |developmental stage:96 hpf|cell type:Epicardial cells,GSM5318591,GSM5318591: EpiCs tcf21 / 96 hpf [Epi Mut 1]; Danio rerio; RNA Seq,GSM5318591,,1,Hearts from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000 1000 cells per replicate were used and total RNA was isolated using the miRNeasy micro kit Qiagen combined with on column DNase digestion. 4 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,GEO Accession:GSM5318591,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP319994,,loader:fastq load.py,Giulia_Lib_Epi_Mut_1_R1.fastq.gz,fastq,3594930318.0,48756790.0,GSM5318591 r1,0:73.73,A:1022761996;C:783088936;G:796848144;T:992217994;N:13248,73,,,,1022761996,783088936,796848144,992217994,13248,SRX10902993,SRS8995268,SRA1232823,GEO,MPI for heart and lung research,1,0.91011,,0.15636,,0.78825,,0.45701,,73,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2021-05-16,Larval,Larval,Heart,Cardiovascular System 64346,SRR14559686,SRX10902992,SRS8995267,SRP319994,PRJNA730305,Identification of Tcf21 downstream genes in the epicardial cells and cardiomyocytes by transcriptomic analysis,GSE174505,Transcriptome Analysis,Purpose: Studying the epicardium myocardium crosstalk in the zebrafish larval heart. To do so we aimed to identify with RNA seq the genes dysregulated following the loss of the epicardial marker gene tcf21 in sorted epicardial cells and cardiomyocytes. Results: We first analyzed the transcriptome of epicardial and myocardial WT cells and identified cell type specific/enriched genes. Then we identified several differential expressed genes in tcf21 mutants including several ligand receptor couples known to mediate the epicardium myocardium crosstalk. Overall design: Hearts were manually extracted from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae. Hearts were dissociated into single cell suspensions and FACS was performed to sort epicardial and myocardial cells based on the fluorescence signal.,,pubmed:36172839,,CMs tcf21+/+ 96 hpf [CM WT 2],GSM5318590,,tissue:Sorted cardiomyocytes|strain:Tgmyl7:mCherry CAAX+ Tgtcf21:nls.EGFP |genotype:tcf21+/+|developmental stage:96 hpf|cell type:Cardiomyocytes,CMs tcf21+/+ 96 hpf [CM WT 2],Trimmomatic version 0.39 was used to trim reads with a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were used in subsequent analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 Ensembl release 99 using STAR 2.7.3a with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package Liao et al. 2014. Only reads mapping at least partially inside exons were admitted and aggregated per gene while reads overlapping multiple genes or aligning to multiple regions were excluded from further analyses. Differentially expressed genes were identified using DESeq2 version 1.26.0 Love et al. 2014. To remove a batch effect from the comparison the replicates were presented to DESeq2 as covariates DMSO 1/Inhib 1 = 1 DMSO 2/Inhib 2 = 2. The Ensembl annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers. Genome build: DanRer11 GRCz11 Supplementary files format and content: counts.matrix.norm anno.txt: Tab delimited text file includes library size normalized counts.,Sorted cardiomyocytes,,Hearts from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000 1000 cells per replicate were used and total RNA was isolated using the miRNeasy micro kit Qiagen combined with on column DNase digestion. 4 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,,strain:Tgmyl7:mCherry CAAX+ Tgtcf21:nls.EGFP |genotype:tcf21+/+|developmental stage:96 hpf|cell type:Cardiomyocytes,GSM5318590,GSM5318590: CMs tcf21+/+ 96 hpf [CM WT 2]; Danio rerio; RNA Seq,GSM5318590,,1,Hearts from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000 1000 cells per replicate were used and total RNA was isolated using the miRNeasy micro kit Qiagen combined with on column DNase digestion. 4 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,GEO Accession:GSM5318590,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP319994,,loader:fastq load.py,Giulia_Lib_CM_WT_2_R1.fastq.gz,fastq,3581607451.0,48771940.0,GSM5318590 r1,0:73.44,A:1004228251;C:800307770;G:813640945;T:963417119;N:13366,73,,,,1004228251,800307770,813640945,963417119,13366,SRX10902992,SRS8995267,SRA1232823,GEO,MPI for heart and lung research,1,0.93484,,0.07055,,0.82134,,0.52578,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2021-05-16,Larval,Larval,Heart,Cardiovascular System 64347,SRR14559685,SRX10902991,SRS8995266,SRP319994,PRJNA730305,Identification of Tcf21 downstream genes in the epicardial cells and cardiomyocytes by transcriptomic analysis,GSE174505,Transcriptome Analysis,Purpose: Studying the epicardium myocardium crosstalk in the zebrafish larval heart. To do so we aimed to identify with RNA seq the genes dysregulated following the loss of the epicardial marker gene tcf21 in sorted epicardial cells and cardiomyocytes. Results: We first analyzed the transcriptome of epicardial and myocardial WT cells and identified cell type specific/enriched genes. Then we identified several differential expressed genes in tcf21 mutants including several ligand receptor couples known to mediate the epicardium myocardium crosstalk. Overall design: Hearts were manually extracted from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae. Hearts were dissociated into single cell suspensions and FACS was performed to sort epicardial and myocardial cells based on the fluorescence signal.,,pubmed:36172839,,CMs tcf21+/+ 96 hpf [CM WT 1],GSM5318589,,tissue:Sorted cardiomyocytes|strain:Tgmyl7:mCherry CAAX+ Tgtcf21:nls.EGFP |genotype:tcf21+/+|developmental stage:96 hpf|cell type:Cardiomyocytes,CMs tcf21+/+ 96 hpf [CM WT 1],Trimmomatic version 0.39 was used to trim reads with a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were used in subsequent analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 Ensembl release 99 using STAR 2.7.3a with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package Liao et al. 2014. Only reads mapping at least partially inside exons were admitted and aggregated per gene while reads overlapping multiple genes or aligning to multiple regions were excluded from further analyses. Differentially expressed genes were identified using DESeq2 version 1.26.0 Love et al. 2014. To remove a batch effect from the comparison the replicates were presented to DESeq2 as covariates DMSO 1/Inhib 1 = 1 DMSO 2/Inhib 2 = 2. The Ensembl annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers. Genome build: DanRer11 GRCz11 Supplementary files format and content: counts.matrix.norm anno.txt: Tab delimited text file includes library size normalized counts.,Sorted cardiomyocytes,,Hearts from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000 1000 cells per replicate were used and total RNA was isolated using the miRNeasy micro kit Qiagen combined with on column DNase digestion. 4 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,,strain:Tgmyl7:mCherry CAAX+ Tgtcf21:nls.EGFP |genotype:tcf21+/+|developmental stage:96 hpf|cell type:Cardiomyocytes,GSM5318589,GSM5318589: CMs tcf21+/+ 96 hpf [CM WT 1]; Danio rerio; RNA Seq,GSM5318589,,1,Hearts from 96 hpf Tgmyl7:mcherry TgBACtcf21:nls EGFP tcf21+/+ and tcf21 / zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000 1000 cells per replicate were used and total RNA was isolated using the miRNeasy micro kit Qiagen combined with on column DNase digestion. 4 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,GEO Accession:GSM5318589,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP319994,,loader:fastq load.py,Giulia_Lib_CM_WT_1_R1.fastq.gz,fastq,3087428108.0,41946179.0,GSM5318589 r1,0:73.60,A:868793593;C:685998857;G:698875758;T:833748566;N:11334,73,,,,868793593,685998857,698875758,833748566,11334,SRX10902991,SRS8995266,SRA1232823,GEO,MPI for heart and lung research,1,0.9279,,0.06113,,0.83597,,0.51844,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2021-05-16,Larval,Larval,Heart,Cardiovascular System 69592,SRR18927196,SRX15004841,SRS12753553,SRP372368,PRJNA832312,Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2,GSE201611,Transcriptome Analysis,The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition,,pubmed:35531980,,FAC sorted GFP cells 15 s Gtendocard:egfp rep 3,GSM6068601,,source name:Endocardium|tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage,FAC sorted GFP cells 15 s Gtendocard:egfp rep 3,Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output,Endocardium,,Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147,Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage,tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage,GSM6068601,GSM6068601: FAC sorted GFP cells 15 s Gtendocard:egfp rep 3; Danio rerio; RNA Seq,GSM6068601 r1,GSM6068601,1,Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP372368,,,endocardegfp_03_S3_L001_R1_001.fastq.gz,fastq,789993899.0,10821883.0,GSM6068601 r1,0:73.00 1:0,A:215890135;C:178235825;G:183043642;T:212180982;N:643315,73,0,,,215890135,178235825,183043642,212180982,643315,SRX15004841,SRS12753553,SRA1410588,"Department of Anatomy & Physiology, The University of Melbourne","Department of Anatomy & Physiology, The University of Melbourne",1,0.94291,,0.0758,,0.75071,,0.46413,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Australia,2022-04-26,Segmentation,Embryo,Heart,Cardiovascular System 69593,SRR18927197,SRX15004841,SRS12753553,SRP372368,PRJNA832312,Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2,GSE201611,Transcriptome Analysis,The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition,,pubmed:35531980,,FAC sorted GFP cells 15 s Gtendocard:egfp rep 3,GSM6068601,,source name:Endocardium|tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage,FAC sorted GFP cells 15 s Gtendocard:egfp rep 3,Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output,Endocardium,,Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147,Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage,tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage,GSM6068601,GSM6068601: FAC sorted GFP cells 15 s Gtendocard:egfp rep 3; Danio rerio; RNA Seq,GSM6068601 r1,GSM6068601,1,Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP372368,,,endocardegfp_03_S3_L002_R1_001.fastq.gz,fastq,761479840.0,10440053.0,GSM6068601 r2,0:72.94 1:0,A:208204230;C:172086666;G:175892087;T:204676185;N:620672,72,0,,,208204230,172086666,175892087,204676185,620672,SRX15004841,SRS12753553,SRA1410588,"Department of Anatomy & Physiology, The University of Melbourne","Department of Anatomy & Physiology, The University of Melbourne",1,0.94452,,0.07485,,0.74998,,0.50338,,38,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Australia,2022-04-26,Segmentation,Embryo,Heart,Cardiovascular System 69594,SRR18927198,SRX15004841,SRS12753553,SRP372368,PRJNA832312,Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2,GSE201611,Transcriptome Analysis,The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition,,pubmed:35531980,,FAC sorted GFP cells 15 s Gtendocard:egfp rep 3,GSM6068601,,source name:Endocardium|tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage,FAC sorted GFP cells 15 s Gtendocard:egfp rep 3,Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output,Endocardium,,Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147,Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage,tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage,GSM6068601,GSM6068601: FAC sorted GFP cells 15 s Gtendocard:egfp rep 3; Danio rerio; RNA Seq,GSM6068601 r1,GSM6068601,1,Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP372368,,,endocardegfp_03_S3_L003_R1_001.fastq.gz,fastq,765660473.0,10491638.0,GSM6068601 r3,0:72.98 1:0,A:209572424;C:172800895;G:176915262;T:205772587;N:599305,72,0,,,209572424,172800895,176915262,205772587,599305,SRX15004841,SRS12753553,SRA1410588,"Department of Anatomy & Physiology, The University of Melbourne","Department of Anatomy & Physiology, The University of Melbourne",1,0.94355,,0.07527,,0.75055,,0.50343,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Australia,2022-04-26,Segmentation,Embryo,Heart,Cardiovascular System 69595,SRR18927199,SRX15004841,SRS12753553,SRP372368,PRJNA832312,Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2,GSE201611,Transcriptome Analysis,The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition,,pubmed:35531980,,FAC sorted GFP cells 15 s Gtendocard:egfp rep 3,GSM6068601,,source name:Endocardium|tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage,FAC sorted GFP cells 15 s Gtendocard:egfp rep 3,Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output,Endocardium,,Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147,Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage,tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage,GSM6068601,GSM6068601: FAC sorted GFP cells 15 s Gtendocard:egfp rep 3; Danio rerio; RNA Seq,GSM6068601 r1,GSM6068601,1,Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP372368,,,endocardegfp_03_S3_L004_R1_001.fastq.gz,fastq,776554362.0,10626636.0,GSM6068601 r4,0:73.08 1:0,A:212610309;C:175329364;G:179249787;T:208800328;N:564574,73,0,,,212610309,175329364,179249787,208800328,564574,SRX15004841,SRS12753553,SRA1410588,"Department of Anatomy & Physiology, The University of Melbourne","Department of Anatomy & Physiology, The University of Melbourne",1,0.94493,,0.07566,,0.74953,,0.50021,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Australia,2022-04-26,Segmentation,Embryo,Heart,Cardiovascular System