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
40164,SRR2921973,SRX1432516,SRS1163508,SRP066192,PRJNA302179,Genome–wide transcriptional profiling with spatial resolution identifies Bone Morphogenetic Protein signaling as essential regulator of zebrafish cardiomyocyte regeneration.,GSE74652,Transcriptome Analysis,In contrast to mammals  zebrafish regenerate heart injuries via proliferation of cardiomyocytes located at the wound border. Here  we show that tomo seq can be used to identify whole genome transcriptional profiles of the injury zone  the border zone and the healthy myocardium. Interestingly  the border zone is characterized by the re expression of embryonic cardiac genes that are also activated post myocardial infarction in mouse and human  including targets of Bone Morphogenetic Protein BMP signaling. Endogenous BMP signaling has been reported to be detrimental to mammalian cardiac repair. In contrast  we find that genetic or chemical inhibition of BMP signaling in zebrafish reduces cardiomyocyte dedifferentiation and proliferation  ultimately compromising myocardial regeneration  while bmp2b overexpression is sufficient to enhance it. Our results provide a resource for further studies on the molecular regulation of cardiac regeneration and reveal intriguing differential cellular responses of cardiomyocytes to a conserved signaling pathway in regenerative versus non regenerative hearts. Overall design: To generate spatially resolved RNA seq data for injured zebrafish hearts 3 and 7 xxx post injury  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina NextSeq  using 75bp paired end sequencing.,,pubmed:26748692,,zebrafish heart WT 7dpi #1,GSM1924888,,source name:cryoinjured ventricle of the heart|tissue:adult heart|sectioning direction:injury area   uninjured  remote myocardium|sectioning thickness:12 µm|embedding strategy:extracted heart at 7 days post cryoinjury,zebrafish heart WT 7dpi #1,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,cryoinjured ventricle of the heart,Unfixed ventricle was embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see: Junker et al.  2014  Cell,,tissue:adult heart|sectioning direction:injury area   uninjured  remote myocardium|sectioning thickness:12 µm|embedding strategy:extracted heart at 7 days post cryoinjury,GSM1924888,GSM1924888: zebrafish heart WT 7dpi #1; Danio rerio; RNA Seq,GSM1924888,,1,RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see: Junker et al.  2014  Cell,GEO Accession:GSM1924888,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP066192,,,FKHEART7_R1.fastq.gz FKHEART7_R2.fastq.gz,fastq fastq,3128649900.0,20745605.0,GSM1924888 r1,0:75.43 1:75.38,A:1025473014;C:388501715;G:410501025;T:1304153289;N:20857,75,75,,,1025473014,388501715,410501025,1304153289,20857,SRX1432516,SRS1163508,SRA311639,GEO,"Jeroen Bakkers, Hubrecht Institute",2,0.31194,0.62458,0.26968,0.18109,0.99308,0.89258,0.54708,0.5286,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,celseq,,Netherlands,2015-11-03,Adult,Adult,Heart,Cardiovascular System
40165,SRR2921972,SRX1432515,SRS1163510,SRP066192,PRJNA302179,Genome–wide transcriptional profiling with spatial resolution identifies Bone Morphogenetic Protein signaling as essential regulator of zebrafish cardiomyocyte regeneration.,GSE74652,Transcriptome Analysis,In contrast to mammals  zebrafish regenerate heart injuries via proliferation of cardiomyocytes located at the wound border. Here  we show that tomo seq can be used to identify whole genome transcriptional profiles of the injury zone  the border zone and the healthy myocardium. Interestingly  the border zone is characterized by the re expression of embryonic cardiac genes that are also activated post myocardial infarction in mouse and human  including targets of Bone Morphogenetic Protein BMP signaling. Endogenous BMP signaling has been reported to be detrimental to mammalian cardiac repair. In contrast  we find that genetic or chemical inhibition of BMP signaling in zebrafish reduces cardiomyocyte dedifferentiation and proliferation  ultimately compromising myocardial regeneration  while bmp2b overexpression is sufficient to enhance it. Our results provide a resource for further studies on the molecular regulation of cardiac regeneration and reveal intriguing differential cellular responses of cardiomyocytes to a conserved signaling pathway in regenerative versus non regenerative hearts. Overall design: To generate spatially resolved RNA seq data for injured zebrafish hearts 3 and 7 xxx post injury  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina NextSeq  using 75bp paired end sequencing.,,pubmed:26748692,,zebrafish heart WT 3dpi #1,GSM1924887,,source name:cryoinjured ventricle of the heart|tissue:adult heart|sectioning direction:injury area   uninjured  remote myocardium|sectioning thickness:12 µm|embedding strategy:extracted heart at 3 days post cryoinjury,zebrafish heart WT 3dpi #1,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,cryoinjured ventricle of the heart,Unfixed ventricle was embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see: Junker et al.  2014  Cell,,tissue:adult heart|sectioning direction:injury area   uninjured  remote myocardium|sectioning thickness:12 µm|embedding strategy:extracted heart at 3 days post cryoinjury,GSM1924887,GSM1924887: zebrafish heart WT 3dpi #1; Danio rerio; RNA Seq,GSM1924887,,1,RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see: Junker et al.  2014  Cell,GEO Accession:GSM1924887,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP066192,,,FKHEART3_R1.fastq.gz FKHEART3_R2.fastq.gz,fastq fastq,784558404.0,5209213.0,GSM1924887 r1,0:75.22 1:75.39,A:291009319;C:102718146;G:111606154;T:279144074;N:80711,75,75,,,291009319,102718146,111606154,279144074,80711,SRX1432515,SRS1163510,SRA311639,GEO,"Jeroen Bakkers, Hubrecht Institute",2,0.12872,0.82031,0.12623,0.08476,0.99997,0.82828,0.0,0.566,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,celseq,,Netherlands,2015-11-03,Adult,Adult,Heart,Cardiovascular System
43755,SRR6054093,SRX3201032,SRS2528004,SRP118319,PRJNA408129,Spatially resolved RNA sequencing of the embryonic zebrafish heart,GSE104057,Transcriptome Analysis,Development of specialized cell types and structures in the vertebrate heart is regulated by spatially restricted molecular pathways. Disruptions in these pathways can cause severe congenital cardiac malformations or functional defects. To better understand these pathways and how they regulate cardiac development and function we used tomo seq  combining high throughput RNA sequencing with tissue sectioning  to establish a genome wide expression dataset with high spatial resolution for the developing zebrafish heart. Analysis of the dataset revealed over 1100 genes differentially expressed in sub compartments. Pacemaker cells in the sinoatrial region induce heart contractions  but little is known about the mechanisms underlying their development and function. Using our transcriptome map  we identified spatially restricted Wnt/ß catenin signaling activity in pacemaker cells  which was controlled by Islet 1 activity. Moreover  Wnt/ß catenin signaling at a specific developmental stage in the myocardium controls heart rate by regulating pacemaker cellular response to parasympathetic stimuli. Thus  this high resolution transcriptome map incorporating all cell types in the embryonic heart can expose spatially restricted molecular pathways critical for specific cardiac functions. Overall design: To generate spatially resolved RNA seq data for the developing zebrafish hearts 2 dpf  we cryosectioned 3 hearts  extracted RNA from the individual sections  amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina NextSeq using 75bp paired end sequencing. Sample Heart #1 is the primary sample. Heart #2 and #3 are biological replicates used for comparison.,,pubmed:29400650,,heart3 2dpf wt,GSM2788520,,source name:isolated embryonic heart|tissue:embryonic heart|developmental stage:48 hpf direction:posterior/inflow tract to anterior/outflow tract; located in sections #11   #39|section thickness:10µm sections,heart3 2dpf wt,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: csv file containing transcript counts per gene rows and section columns,isolated embryonic heart,Unfixed embryonic hearts were dissected and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012  see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:embryonic heart|developmental stage:48 hpf direction:posterior/inflow tract to anterior/outflow tract; located in sections #11   #39|section thickness:10µm sections,GSM2788520,GSM2788520: heart3 2dpf wt; Danio rerio; RNA Seq,GSM2788520,,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012  see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,GEO Accession:GSM2788520,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP118319,,,heart_03_SB032dpfwt_R1.fastq.gz heart_03_SB032dpfwt_R2.fastq.gz,fastq fastq,2662906147.0,17670214.0,GSM2788520 r1,0:75.39 1:75.31,A:828280216;C:376671462;G:437493213;T:1019745554;N:715702,75,75,,,828280216,376671462,437493213,1019745554,715702,SRX3201032,SRS2528004,SRA610777,GEO,"Jeroen Bakkers lab, Cardiac Development and Genetics, Hubrecht Institute",2,0.04145,0.36579,0.03839,0.09603,0.99912,0.89623,0.41379,0.5674,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2017-09-20,Hatching,Embryo,Heart,Cardiovascular System
43756,SRR6054092,SRX3201031,SRS2528003,SRP118319,PRJNA408129,Spatially resolved RNA sequencing of the embryonic zebrafish heart,GSE104057,Transcriptome Analysis,Development of specialized cell types and structures in the vertebrate heart is regulated by spatially restricted molecular pathways. Disruptions in these pathways can cause severe congenital cardiac malformations or functional defects. To better understand these pathways and how they regulate cardiac development and function we used tomo seq  combining high throughput RNA sequencing with tissue sectioning  to establish a genome wide expression dataset with high spatial resolution for the developing zebrafish heart. Analysis of the dataset revealed over 1100 genes differentially expressed in sub compartments. Pacemaker cells in the sinoatrial region induce heart contractions  but little is known about the mechanisms underlying their development and function. Using our transcriptome map  we identified spatially restricted Wnt/ß catenin signaling activity in pacemaker cells  which was controlled by Islet 1 activity. Moreover  Wnt/ß catenin signaling at a specific developmental stage in the myocardium controls heart rate by regulating pacemaker cellular response to parasympathetic stimuli. Thus  this high resolution transcriptome map incorporating all cell types in the embryonic heart can expose spatially restricted molecular pathways critical for specific cardiac functions. Overall design: To generate spatially resolved RNA seq data for the developing zebrafish hearts 2 dpf  we cryosectioned 3 hearts  extracted RNA from the individual sections  amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina NextSeq using 75bp paired end sequencing. Sample Heart #1 is the primary sample. Heart #2 and #3 are biological replicates used for comparison.,,pubmed:29400650,,heart2 2dpf wt,GSM2788519,,source name:isolated embryonic heart|tissue:embryonic heart|developmental stage:48 hpf direction:posterior/inflow tract to anterior/outflow tract; located in sections #49   #96|section thickness:10µm sections,heart2 2dpf wt,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: csv file containing transcript counts per gene rows and section columns,isolated embryonic heart,Unfixed embryonic hearts were dissected and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012  see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:embryonic heart|developmental stage:48 hpf direction:posterior/inflow tract to anterior/outflow tract; located in sections #49   #96|section thickness:10µm sections,GSM2788519,GSM2788519: heart2 2dpf wt; Danio rerio; RNA Seq,GSM2788519,,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012  see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,GEO Accession:GSM2788519,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP118319,,,heart_02_SB-150707_R1.fastq.gz heart_02_SB-150707_R2.fastq.gz,fastq fastq,5482437730.0,36337096.0,GSM2788519 r1,0:75.41 1:75.47,A:1859596349;C:686627791;G:950285046;T:1980208127;N:5720417,75,75,,,1859596349,686627791,950285046,1980208127,5720417,SRX3201031,SRS2528003,SRA610777,GEO,"Jeroen Bakkers lab, Cardiac Development and Genetics, Hubrecht Institute",2,0.14301,0.55835,0.12504,0.16935,0.99285,0.86334,0.46837,0.58661,76,74,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2017-09-20,Hatching,Embryo,Heart,Cardiovascular System
43757,SRR6054091,SRX3201030,SRS2528002,SRP118319,PRJNA408129,Spatially resolved RNA sequencing of the embryonic zebrafish heart,GSE104057,Transcriptome Analysis,Development of specialized cell types and structures in the vertebrate heart is regulated by spatially restricted molecular pathways. Disruptions in these pathways can cause severe congenital cardiac malformations or functional defects. To better understand these pathways and how they regulate cardiac development and function we used tomo seq  combining high throughput RNA sequencing with tissue sectioning  to establish a genome wide expression dataset with high spatial resolution for the developing zebrafish heart. Analysis of the dataset revealed over 1100 genes differentially expressed in sub compartments. Pacemaker cells in the sinoatrial region induce heart contractions  but little is known about the mechanisms underlying their development and function. Using our transcriptome map  we identified spatially restricted Wnt/ß catenin signaling activity in pacemaker cells  which was controlled by Islet 1 activity. Moreover  Wnt/ß catenin signaling at a specific developmental stage in the myocardium controls heart rate by regulating pacemaker cellular response to parasympathetic stimuli. Thus  this high resolution transcriptome map incorporating all cell types in the embryonic heart can expose spatially restricted molecular pathways critical for specific cardiac functions. Overall design: To generate spatially resolved RNA seq data for the developing zebrafish hearts 2 dpf  we cryosectioned 3 hearts  extracted RNA from the individual sections  amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina NextSeq using 75bp paired end sequencing. Sample Heart #1 is the primary sample. Heart #2 and #3 are biological replicates used for comparison.,,pubmed:29400650,,heart1 2dpf wt,GSM2788518,,source name:isolated embryonic heart|tissue:embryonic heart|developmental stage:48 hpf direction:anterior/outflow tract to posterior/inflow tract; located in sections #2   #41|section thickness:10µm sections,heart1 2dpf wt,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: csv file containing transcript counts per gene rows and section columns,isolated embryonic heart,Unfixed embryonic hearts were dissected and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012  see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,tissue:embryonic heart|developmental stage:48 hpf direction:anterior/outflow tract to posterior/inflow tract; located in sections #2   #41|section thickness:10µm sections,GSM2788518,GSM2788518: heart1 2dpf wt; Danio rerio; RNA Seq,GSM2788518,,1,Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012  see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,GEO Accession:GSM2788518,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP118319,,,heart_01_SB-06-2dpf_wt_R2.fastq.gz heart_01_SB-06-2dpf_wt_R1.fastq.gz,fastq fastq,8152229052.0,54104958.0,GSM2788518 r1,0:75.41 1:75.27,A:2955268830;C:1118145970;G:1152323290;T:2924136690;N:2354272,75,75,,,2955268830,1118145970,1152323290,2924136690,2354272,SRX3201030,SRS2528002,SRA610777,GEO,"Jeroen Bakkers lab, Cardiac Development and Genetics, Hubrecht Institute",2,0.02706,0.26955,0.01984,0.05871,0.99675,0.93194,0.37979,0.63172,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2017-09-20,Hatching,Embryo,Heart,Cardiovascular System
48190,SRR7119875,SRX4041518,SRS3258997,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 3dpf mut 44,GSM3131266,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 3dpf mut 44,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ,GSM3131266,GSM3131266: Danio rerio RNAseq singleHeart 3dpf mut 44; Danio rerio; RNA Seq,GSM3131266,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131266,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_44_NDCII_sample_0044.fastq.gz,fastq,182748450.0,2436646.0,GSM3131266 r1,0:75,A:58073626;C:30410206;G:39711272;T:54442336;N:111010,75,,,,58073626,30410206,39711272,54442336,111010,SRX4041518,SRS3258997,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.60972,,0.21593,,0.85427,,0.51332,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Heart,Cardiovascular System
48191,SRR7119874,SRX4041517,SRS3258996,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 3dpf mut 43,GSM3131265,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 3dpf mut 43,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ,GSM3131265,GSM3131265: Danio rerio RNAseq singleHeart 3dpf mut 43; Danio rerio; RNA Seq,GSM3131265,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131265,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_43_NDCII_sample_0043.fastq.gz,fastq,91153575.0,1215381.0,GSM3131265 r1,0:75,A:29202562;C:14935465;G:19738048;T:27228137;N:49363,75,,,,29202562,14935465,19738048,27228137,49363,SRX4041517,SRS3258996,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.61061,,0.18268,,0.87257,,0.51994,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Heart,Cardiovascular System
48192,SRR7119873,SRX4041516,SRS3258995,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 3dpf mut 42,GSM3131264,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 3dpf mut 42,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ,GSM3131264,GSM3131264: Danio rerio RNAseq singleHeart 3dpf mut 42; Danio rerio; RNA Seq,GSM3131264,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131264,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_42_NDCII_sample_0042.fastq.gz,fastq,213129525.0,2841727.0,GSM3131264 r1,0:75,A:66201701;C:36179557;G:46211697;T:64412897;N:123673,75,,,,66201701,36179557,46211697,64412897,123673,SRX4041516,SRS3258995,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.62509,,0.23068,,0.85397,,0.4951,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Heart,Cardiovascular System
48193,SRR7119872,SRX4041515,SRS3258994,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 3dpf mut 41,GSM3131263,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 3dpf mut 41,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ,GSM3131263,GSM3131263: Danio rerio RNAseq singleHeart 3dpf mut 41; Danio rerio; RNA Seq,GSM3131263,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131263,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_41_NDCII_sample_0041.fastq.gz,fastq,166984800.0,2226464.0,GSM3131263 r1,0:75,A:52059221;C:28218639;G:36132669;T:50478431;N:95840,75,,,,52059221,28218639,36132669,50478431,95840,SRX4041515,SRS3258994,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.64245,,0.22817,,0.86535,,0.4946,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Heart,Cardiovascular System
48194,SRR7119871,SRX4041514,SRS3258992,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 3dpf mut 40,GSM3131262,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 3dpf mut 40,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ,GSM3131262,GSM3131262: Danio rerio RNAseq singleHeart 3dpf mut 40; Danio rerio; RNA Seq,GSM3131262,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131262,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_40_NDCII_sample_0040.fastq.gz,fastq,76091325.0,1014551.0,GSM3131262 r1,0:75,A:23961767;C:13365431;G:16139381;T:22578835;N:45911,75,,,,23961767,13365431,16139381,22578835,45911,SRX4041514,SRS3258992,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.68263,,0.15501,,0.86642,,0.45686,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Heart,Cardiovascular System
48195,SRR7119870,SRX4041513,SRS3258993,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 3dpf mut 39,GSM3131261,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 3dpf mut 39,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ,GSM3131261,GSM3131261: Danio rerio RNAseq singleHeart 3dpf mut 39; Danio rerio; RNA Seq,GSM3131261,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131261,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_39_NDCII_sample_0039.fastq.gz,fastq,83697825.0,1115971.0,GSM3131261 r1,0:75,A:25833162;C:14319026;G:18237724;T:25260425;N:47488,75,,,,25833162,14319026,18237724,25260425,47488,SRX4041513,SRS3258993,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.68511,,0.1681,,0.87359,,0.50056,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Heart,Cardiovascular System
48196,SRR7119869,SRX4041512,SRS3258991,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 3dpf mut 38,GSM3131260,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 3dpf mut 38,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ,GSM3131260,GSM3131260: Danio rerio RNAseq singleHeart 3dpf mut 38; Danio rerio; RNA Seq,GSM3131260,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131260,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_38_NDCII_sample_0038.fastq.gz,fastq,89200050.0,1189334.0,GSM3131260 r1,0:75,A:27880894;C:15422868;G:19386687;T:26456153;N:53448,75,,,,27880894,15422868,19386687,26456153,53448,SRX4041512,SRS3258991,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.63181,,0.17615,,0.86736,,0.5058,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Heart,Cardiovascular System
48197,SRR7119868,SRX4041511,SRS3258989,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 3dpf mut 37,GSM3131259,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 3dpf mut 37,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ,GSM3131259,GSM3131259: Danio rerio RNAseq singleHeart 3dpf mut 37; Danio rerio; RNA Seq,GSM3131259,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131259,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_37_NDCII_sample_0037.fastq.gz,fastq,144136050.0,1921814.0,GSM3131259 r1,0:75,A:45236020;C:23884461;G:31356238;T:43570898;N:88433,75,,,,45236020,23884461,31356238,43570898,88433,SRX4041511,SRS3258989,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.64128,,0.19693,,0.86734,,0.54791,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Heart,Cardiovascular System
48198,SRR7119867,SRX4041510,SRS3258990,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 3dpf mut 36,GSM3131258,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 3dpf mut 36,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ,GSM3131258,GSM3131258: Danio rerio RNAseq singleHeart 3dpf mut 36; Danio rerio; RNA Seq,GSM3131258,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131258,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_36_NDCII_sample_0036.fastq.gz,fastq,98485275.0,1313137.0,GSM3131258 r1,0:75,A:31078665;C:16821229;G:21507034;T:29019964;N:58383,75,,,,31078665,16821229,21507034,29019964,58383,SRX4041510,SRS3258990,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.62906,,0.24825,,0.86592,,0.56159,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Heart,Cardiovascular System
48199,SRR7119866,SRX4041509,SRS3258988,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf mut 35,GSM3131257,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 2dpf mut 35,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ,GSM3131257,GSM3131257: Danio rerio RNAseq singleHeart 2dpf mut 35; Danio rerio; RNA Seq,GSM3131257,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131257,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_35_NDCII_sample_0035.fastq.gz,fastq,137582100.0,1834428.0,GSM3131257 r1,0:75,A:42420010;C:23366189;G:30187957;T:41528798;N:79146,75,,,,42420010,23366189,30187957,41528798,79146,SRX4041509,SRS3258988,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.69634,,0.15154,,0.85827,,0.50259,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48200,SRR7119865,SRX4041508,SRS3258987,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf mut 34,GSM3131256,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 2dpf mut 34,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ,GSM3131256,GSM3131256: Danio rerio RNAseq singleHeart 2dpf mut 34; Danio rerio; RNA Seq,GSM3131256,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131256,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_34_NDCII_sample_0034.fastq.gz,fastq,115231725.0,1536423.0,GSM3131256 r1,0:75,A:36189151;C:19748534;G:25280516;T:33944039;N:69485,75,,,,36189151,19748534,25280516,33944039,69485,SRX4041508,SRS3258987,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.65755,,0.14147,,0.8635,,0.53314,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48201,SRR7119864,SRX4041507,SRS3258986,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf mut 33,GSM3131255,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 2dpf mut 33,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ,GSM3131255,GSM3131255: Danio rerio RNAseq singleHeart 2dpf mut 33; Danio rerio; RNA Seq,GSM3131255,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131255,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_33_NDCII_sample_0033.fastq.gz,fastq,86985525.0,1159807.0,GSM3131255 r1,0:75,A:27397325;C:14512545;G:19080050;T:25941403;N:54202,75,,,,27397325,14512545,19080050,25941403,54202,SRX4041507,SRS3258986,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.63426,,0.16676,,0.87568,,0.5457,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48202,SRR7119863,SRX4041506,SRS3258985,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf mut 32,GSM3131254,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 2dpf mut 32,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ,GSM3131254,GSM3131254: Danio rerio RNAseq singleHeart 2dpf mut 32; Danio rerio; RNA Seq,GSM3131254,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131254,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_32_NDCII_sample_0032.fastq.gz,fastq,64224375.0,856325.0,GSM3131254 r1,0:75,A:20154725;C:11180349;G:13983116;T:18869397;N:36788,75,,,,20154725,11180349,13983116,18869397,36788,SRX4041506,SRS3258985,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.65978,,0.16164,,0.8775,,0.54741,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48203,SRR7119862,SRX4041505,SRS3258984,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf mut 31,GSM3131253,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 2dpf mut 31,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ,GSM3131253,GSM3131253: Danio rerio RNAseq singleHeart 2dpf mut 31; Danio rerio; RNA Seq,GSM3131253,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131253,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_31_NDCII_sample_0031.fastq.gz,fastq,159901350.0,2132018.0,GSM3131253 r1,0:75,A:50993443;C:26156045;G:34865968;T:47792042;N:93852,75,,,,50993443,26156045,34865968,47792042,93852,SRX4041505,SRS3258984,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.6343,,0.22382,,0.84707,,0.44037,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48204,SRR7119861,SRX4041504,SRS3258983,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf mut 29,GSM3131252,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 2dpf mut 29,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ,GSM3131252,GSM3131252: Danio rerio RNAseq singleHeart 2dpf mut 29; Danio rerio; RNA Seq,GSM3131252,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131252,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_29_NDCII_sample_0029.fastq.gz,fastq,205405950.0,2738746.0,GSM3131252 r1,0:75,A:64163069;C:34538013;G:45210194;T:61373525;N:121149,75,,,,64163069,34538013,45210194,61373525,121149,SRX4041504,SRS3258983,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.65436,,0.20449,,0.84831,,0.52226,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48205,SRR7119860,SRX4041503,SRS3258982,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf mut 28,GSM3131251,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 2dpf mut 28,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ,GSM3131251,GSM3131251: Danio rerio RNAseq singleHeart 2dpf mut 28; Danio rerio; RNA Seq,GSM3131251,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131251,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_28_NDCII_sample_0028.fastq.gz,fastq,88773525.0,1183647.0,GSM3131251 r1,0:75,A:27560501;C:15646178;G:19351624;T:26163900;N:51322,75,,,,27560501,15646178,19351624,26163900,51322,SRX4041503,SRS3258982,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.67182,,0.16278,,0.86527,,0.53604,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48206,SRR7119859,SRX4041502,SRS3258981,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf mut 27,GSM3131250,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 2dpf mut 27,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ,GSM3131250,GSM3131250: Danio rerio RNAseq singleHeart 2dpf mut 27; Danio rerio; RNA Seq,GSM3131250,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131250,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_27_NDCII_sample_0027.fastq.gz,fastq,135825300.0,1811004.0,GSM3131250 r1,0:75,A:42874929;C:23016416;G:29588893;T:40267147;N:77915,75,,,,42874929,23016416,29588893,40267147,77915,SRX4041502,SRS3258981,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.64606,,0.13997,,0.86401,,0.53196,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48207,SRR7119858,SRX4041501,SRS3258980,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf mut 26,GSM3131249,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 2dpf mut 26,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2 / ,GSM3131249,GSM3131249: Danio rerio RNAseq singleHeart 2dpf mut 26; Danio rerio; RNA Seq,GSM3131249,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131249,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_26_NDCII_sample_0026.fastq.gz,fastq,70861500.0,944820.0,GSM3131249 r1,0:75,A:22209781;C:12313683;G:15411508;T:20885853;N:40675,75,,,,22209781,12313683,15411508,20885853,40675,SRX4041501,SRS3258980,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.65979,,0.17285,,0.8687,,0.51907,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48208,SRR7119857,SRX4041500,SRS3258979,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 3dpf wt 24,GSM3131248,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 3dpf wt 24,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,GSM3131248,GSM3131248: Danio rerio RNAseq singleHeart 3dpf wt 24; Danio rerio; RNA Seq,GSM3131248,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131248,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_24_NDCII_sample_0024.fastq.gz,fastq,56268825.0,750251.0,GSM3131248 r1,0:75,A:17328594;C:9907009;G:12451765;T:16549368;N:32089,75,,,,17328594,9907009,12451765,16549368,32089,SRX4041500,SRS3258979,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.68698,,0.13156,,0.87647,,0.54659,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Heart,Cardiovascular System
48209,SRR7119856,SRX4041499,SRS3258978,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 3dpf wt 23,GSM3131247,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 3dpf wt 23,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,GSM3131247,GSM3131247: Danio rerio RNAseq singleHeart 3dpf wt 23; Danio rerio; RNA Seq,GSM3131247,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131247,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_23_NDCII_sample_0023.fastq.gz,fastq,113729700.0,1516396.0,GSM3131247 r1,0:75,A:34708329;C:19742375;G:24997702;T:34216965;N:64329,75,,,,34708329,19742375,24997702,34216965,64329,SRX4041499,SRS3258978,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.68965,,0.1358,,0.86168,,0.50041,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Heart,Cardiovascular System
48210,SRR7119855,SRX4041498,SRS3258976,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 3dpf wt 22,GSM3131246,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 3dpf wt 22,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,GSM3131246,GSM3131246: Danio rerio RNAseq singleHeart 3dpf wt 22; Danio rerio; RNA Seq,GSM3131246,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131246,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_22_NDCII_sample_0022.fastq.gz,fastq,129788625.0,1730515.0,GSM3131246 r1,0:75,A:39826852;C:22345144;G:28340986;T:39198043;N:77600,75,,,,39826852,22345144,28340986,39198043,77600,SRX4041498,SRS3258976,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.68637,,0.19709,,0.85662,,0.52926,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Heart,Cardiovascular System
48211,SRR7119854,SRX4041497,SRS3258975,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 3dpf wt 21,GSM3131245,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 3dpf wt 21,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,GSM3131245,GSM3131245: Danio rerio RNAseq singleHeart 3dpf wt 21; Danio rerio; RNA Seq,GSM3131245,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131245,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_21_NDCII_sample_0021.fastq.gz,fastq,74830575.0,997741.0,GSM3131245 r1,0:75,A:23292108;C:12771005;G:16485526;T:22236863;N:45073,75,,,,23292108,12771005,16485526,22236863,45073,SRX4041497,SRS3258975,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.62409,,0.23647,,0.88398,,0.52649,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Heart,Cardiovascular System
48212,SRR7119853,SRX4041496,SRS3258974,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 3dpf wt 20,GSM3131244,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 3dpf wt 20,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,GSM3131244,GSM3131244: Danio rerio RNAseq singleHeart 3dpf wt 20; Danio rerio; RNA Seq,GSM3131244,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131244,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_20_NDCII_sample_0020.fastq.gz,fastq,83202075.0,1109361.0,GSM3131244 r1,0:75,A:26090654;C:14537361;G:18178302;T:24348215;N:47543,75,,,,26090654,14537361,18178302,24348215,47543,SRX4041496,SRS3258974,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.59091,,0.18382,,0.87274,,0.50189,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Heart,Cardiovascular System
48213,SRR7119852,SRX4041495,SRS3258973,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 3dpf wt 19,GSM3131243,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 3dpf wt 19,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,GSM3131243,GSM3131243: Danio rerio RNAseq singleHeart 3dpf wt 19; Danio rerio; RNA Seq,GSM3131243,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131243,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_19_NDCII_sample_0019.fastq.gz,fastq,61352025.0,818027.0,GSM3131243 r1,0:75,A:19173237;C:10426603;G:13570586;T:18144746;N:36853,75,,,,19173237,10426603,13570586,18144746,36853,SRX4041495,SRS3258973,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.64995,,0.19171,,0.87213,,0.54952,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Heart,Cardiovascular System
48214,SRR7119851,SRX4041494,SRS3258972,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 3dpf wt 18,GSM3131242,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 3dpf wt 18,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,GSM3131242,GSM3131242: Danio rerio RNAseq singleHeart 3dpf wt 18; Danio rerio; RNA Seq,GSM3131242,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131242,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_18_NDCII_sample_0018.fastq.gz,fastq,55114425.0,734859.0,GSM3131242 r1,0:75,A:17302961;C:9444084;G:12256958;T:16079162;N:31260,75,,,,17302961,9444084,12256958,16079162,31260,SRX4041494,SRS3258972,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.64027,,0.2383,,0.87903,,0.53857,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Heart,Cardiovascular System
48215,SRR7119850,SRX4041493,SRS3258971,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 3dpf wt 17,GSM3131241,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 3dpf wt 17,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,GSM3131241,GSM3131241: Danio rerio RNAseq singleHeart 3dpf wt 17; Danio rerio; RNA Seq,GSM3131241,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131241,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_17_NDCII_sample_0017.fastq.gz,fastq,54385575.0,725141.0,GSM3131241 r1,0:75,A:17178884;C:9154385;G:11956346;T:16062768;N:33192,75,,,,17178884,9154385,11956346,16062768,33192,SRX4041493,SRS3258971,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.6122,,0.27421,,0.88552,,0.5705,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Heart,Cardiovascular System
48216,SRR7119849,SRX4041492,SRS3258970,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 3dpf wt 16,GSM3131240,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 3dpf wt 16,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,GSM3131240,GSM3131240: Danio rerio RNAseq singleHeart 3dpf wt 16; Danio rerio; RNA Seq,GSM3131240,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131240,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_16_NDCII_sample_0016.fastq.gz,fastq,68361225.0,911483.0,GSM3131240 r1,0:75,A:20763268;C:11958924;G:16351810;T:19246084;N:41139,75,,,,20763268,11958924,16351810,19246084,41139,SRX4041492,SRS3258970,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.64264,,0.12251,,0.88477,,0.57059,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Heart,Cardiovascular System
48217,SRR7119848,SRX4041491,SRS3258969,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 3dpf wt 15,GSM3131239,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 3dpf wt 15,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+,GSM3131239,GSM3131239: Danio rerio RNAseq singleHeart 3dpf wt 15; Danio rerio; RNA Seq,GSM3131239,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131239,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_15_NDCII_sample_0015.fastq.gz,fastq,43246350.0,576618.0,GSM3131239 r1,0:75,A:13423239;C:7409151;G:9733956;T:12657584;N:22420,75,,,,13423239,7409151,9733956,12657584,22420,SRX4041491,SRS3258969,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.66495,,0.14227,,0.88828,,0.56869,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Larval,Larval,Heart,Cardiovascular System
48218,SRR7119847,SRX4041490,SRS3258968,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf wt 14,GSM3131238,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 2dpf wt 14,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,GSM3131238,GSM3131238: Danio rerio RNAseq singleHeart 2dpf wt 14; Danio rerio; RNA Seq,GSM3131238,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131238,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_14_NDCII_sample_0014.fastq.gz,fastq,81736125.0,1089815.0,GSM3131238 r1,0:75,A:25374411;C:14225355;G:17601172;T:24489651;N:45536,75,,,,25374411,14225355,17601172,24489651,45536,SRX4041490,SRS3258968,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.68142,,0.17857,,0.86965,,0.53118,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48219,SRR7119846,SRX4041489,SRS3258967,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf wt 13,GSM3131237,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 2dpf wt 13,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,GSM3131237,GSM3131237: Danio rerio RNAseq singleHeart 2dpf wt 13; Danio rerio; RNA Seq,GSM3131237,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131237,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_13_NDCII_sample_0013.fastq.gz,fastq,62250900.0,830012.0,GSM3131237 r1,0:75,A:19221325;C:10606446;G:13851770;T:18535596;N:35763,75,,,,19221325,10606446,13851770,18535596,35763,SRX4041489,SRS3258967,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.67033,,0.16463,,0.88669,,0.52197,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48220,SRR7119845,SRX4041488,SRS3258966,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf wt 12,GSM3131236,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 2dpf wt 12,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,GSM3131236,GSM3131236: Danio rerio RNAseq singleHeart 2dpf wt 12; Danio rerio; RNA Seq,GSM3131236,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131236,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_12_NDCII_sample_0012.fastq.gz,fastq,65079975.0,867733.0,GSM3131236 r1,0:75,A:20574087;C:11008240;G:14305699;T:19155761;N:36188,75,,,,20574087,11008240,14305699,19155761,36188,SRX4041488,SRS3258966,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.65516,,0.23525,,0.87227,,0.55436,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48221,SRR7119844,SRX4041487,SRS3258965,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf wt 11,GSM3131235,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 2dpf wt 11,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,GSM3131235,GSM3131235: Danio rerio RNAseq singleHeart 2dpf wt 11; Danio rerio; RNA Seq,GSM3131235,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131235,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_11_NDCII_sample_0011.fastq.gz,fastq,56312400.0,750832.0,GSM3131235 r1,0:75,A:17682751;C:9499488;G:12398396;T:16701718;N:30047,75,,,,17682751,9499488,12398396,16701718,30047,SRX4041487,SRS3258965,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.66642,,0.21243,,0.87868,,0.52403,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48222,SRR7119843,SRX4041486,SRS3258964,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf wt 10,GSM3131234,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 2dpf wt 10,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,GSM3131234,GSM3131234: Danio rerio RNAseq singleHeart 2dpf wt 10; Danio rerio; RNA Seq,GSM3131234,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131234,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_10_NDCII_sample_0010.fastq.gz,fastq,51364950.0,684866.0,GSM3131234 r1,0:75,A:16163832;C:8838505;G:11290003;T:15043422;N:29188,75,,,,16163832,8838505,11290003,15043422,29188,SRX4041486,SRS3258964,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.65278,,0.18749,,0.87722,,0.53824,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48223,SRR7119842,SRX4041485,SRS3258963,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf wt 9,GSM3131233,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 2dpf wt 9,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,GSM3131233,GSM3131233: Danio rerio RNAseq singleHeart 2dpf wt 9; Danio rerio; RNA Seq,GSM3131233,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131233,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_9_NDCII_sample_0009.fastq.gz,fastq,149036325.0,1987151.0,GSM3131233 r1,0:75,A:47706695;C:23942760;G:33072602;T:44228491;N:85777,75,,,,47706695,23942760,33072602,44228491,85777,SRX4041485,SRS3258963,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.56223,,0.19674,,0.87079,,0.52559,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48224,SRR7119841,SRX4041484,SRS3258962,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf wt 8,GSM3131232,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 2dpf wt 8,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,GSM3131232,GSM3131232: Danio rerio RNAseq singleHeart 2dpf wt 8; Danio rerio; RNA Seq,GSM3131232,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131232,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_8_NDCII_sample_0008.fastq.gz,fastq,61857375.0,824765.0,GSM3131232 r1,0:75,A:19180813;C:10701206;G:13569705;T:18368818;N:36833,75,,,,19180813,10701206,13569705,18368818,36833,SRX4041484,SRS3258962,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.68869,,0.14177,,0.86722,,0.50808,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48225,SRR7119840,SRX4041483,SRS3258960,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf wt 7,GSM3131231,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 2dpf wt 7,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,GSM3131231,GSM3131231: Danio rerio RNAseq singleHeart 2dpf wt 7; Danio rerio; RNA Seq,GSM3131231,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131231,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_7_NDCII_sample_0007.fastq.gz,fastq,34999125.0,466655.0,GSM3131231 r1,0:75,A:10839927;C:6031095;G:7710789;T:10397147;N:20167,75,,,,10839927,6031095,7710789,10397147,20167,SRX4041483,SRS3258960,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.67853,,0.1345,,0.89727,,0.42905,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48226,SRR7119839,SRX4041482,SRS3258959,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf wt 6,GSM3131230,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 2dpf wt 6,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,GSM3131230,GSM3131230: Danio rerio RNAseq singleHeart 2dpf wt 6; Danio rerio; RNA Seq,GSM3131230,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131230,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_6_NDCII_sample_0006.fastq.gz,fastq,53258025.0,710107.0,GSM3131230 r1,0:75,A:16706696;C:9150576;G:11345601;T:16024331;N:30821,75,,,,16706696,9150576,11345601,16024331,30821,SRX4041482,SRS3258959,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.6829,,0.14834,,0.87799,,0.49352,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48227,SRR7119838,SRX4041481,SRS3258958,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf wt 5,GSM3131229,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 2dpf wt 5,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,GSM3131229,GSM3131229: Danio rerio RNAseq singleHeart 2dpf wt 5; Danio rerio; RNA Seq,GSM3131229,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131229,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_5_NDCII_sample_0005.fastq.gz,fastq,46391850.0,618558.0,GSM3131229 r1,0:75,A:14186549;C:7964105;G:10302794;T:13910329;N:28073,75,,,,14186549,7964105,10302794,13910329,28073,SRX4041481,SRS3258958,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.67937,,0.14832,,0.88274,,0.51203,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48228,SRR7119837,SRX4041480,SRS3258957,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf wt 4,GSM3131228,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 2dpf wt 4,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,GSM3131228,GSM3131228: Danio rerio RNAseq singleHeart 2dpf wt 4; Danio rerio; RNA Seq,GSM3131228,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131228,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_4_NDCII_sample_0004.fastq.gz,fastq,119548650.0,1593982.0,GSM3131228 r1,0:75,A:37089578;C:20710248;G:25820048;T:35861658;N:67118,75,,,,37089578,20710248,25820048,35861658,67118,SRX4041480,SRS3258957,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.67925,,0.18634,,0.84431,,0.49844,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48229,SRR7119836,SRX4041479,SRS3258956,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf wt 3,GSM3131227,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 2dpf wt 3,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,GSM3131227,GSM3131227: Danio rerio RNAseq singleHeart 2dpf wt 3; Danio rerio; RNA Seq,GSM3131227,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131227,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_3_NDCII_sample_0003.fastq.gz,fastq,52534500.0,700460.0,GSM3131227 r1,0:75,A:16258360;C:8995544;G:11338397;T:15914972;N:27227,75,,,,16258360,8995544,11338397,15914972,27227,SRX4041479,SRS3258956,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.68677,,0.14664,,0.87541,,0.49296,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48230,SRR7119835,SRX4041478,SRS3258955,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 2dpf wt 2,GSM3131226,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 2dpf wt 2,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:2dpf|genotype:myl7:GFP rnf2+/+,GSM3131226,GSM3131226: Danio rerio RNAseq singleHeart 2dpf wt 2; Danio rerio; RNA Seq,GSM3131226,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131226,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,NDCII_1_2_NDCII_sample_0002.fastq.gz,fastq,27282075.0,363761.0,GSM3131226 r1,0:75,A:8540828;C:4756416;G:5793210;T:8176534;N:15087,75,,,,8540828,4756416,5793210,8176534,15087,SRX4041478,SRS3258955,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.689,,0.16716,,0.89512,,0.51016,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Hatching,Embryo,Heart,Cardiovascular System
48231,SRR7119834,SRX4041477,SRS3259001,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 1dpf mut 9,GSM3131225,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 1dpf mut 9,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / ,GSM3131225,GSM3131225: Danio rerio RNAseq singleHeart 1dpf mut 9; Danio rerio; RNA Seq,GSM3131225,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131225,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,mut_1_9_NDCII_sample_0023.fastq.gz,fastq,57070136.0,762325.0,GSM3131225 r1,0:74.86,A:18605697;C:9652744;G:12793849;T:15973861;N:43985,74,,,,18605697,9652744,12793849,15973861,43985,SRX4041477,SRS3259001,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.65648,,0.53947,,0.94448,,0.46511,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Pharyngula,Embryo,Heart,Cardiovascular System
48232,SRR7119833,SRX4041476,SRS3258954,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 1dpf mut 7,GSM3131224,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 1dpf mut 7,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / ,GSM3131224,GSM3131224: Danio rerio RNAseq singleHeart 1dpf mut 7; Danio rerio; RNA Seq,GSM3131224,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131224,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,mut_1_7_NDCII_sample_0020.fastq.gz,fastq,95756013.0,1278688.0,GSM3131224 r1,0:74.89,A:31571219;C:16875591;G:19112888;T:28125288;N:71027,74,,,,31571219,16875591,19112888,28125288,71027,SRX4041476,SRS3258954,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.77787,,0.38573,,0.89491,,0.52033,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Pharyngula,Embryo,Heart,Cardiovascular System
48233,SRR7119832,SRX4041475,SRS3258953,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 1dpf mut 6,GSM3131223,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 1dpf mut 6,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / ,GSM3131223,GSM3131223: Danio rerio RNAseq singleHeart 1dpf mut 6; Danio rerio; RNA Seq,GSM3131223,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131223,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,mut_1_6_NDCII_sample_0019.fastq.gz,fastq,42326230.0,565166.0,GSM3131223 r1,0:74.89,A:13786789;C:7205959;G:8673068;T:12629903;N:30511,74,,,,13786789,7205959,8673068,12629903,30511,SRX4041475,SRS3258953,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.81231,,0.24386,,0.91662,,0.54902,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Pharyngula,Embryo,Heart,Cardiovascular System
48234,SRR7119831,SRX4041474,SRS3258952,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 1dpf mut 5,GSM3131222,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 1dpf mut 5,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / ,GSM3131222,GSM3131222: Danio rerio RNAseq singleHeart 1dpf mut 5; Danio rerio; RNA Seq,GSM3131222,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131222,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,mut_1_5_NDCII_sample_0018.fastq.gz,fastq,19727283.0,263414.0,GSM3131222 r1,0:74.89,A:6628087;C:3386996;G:3817542;T:5879595;N:15063,74,,,,6628087,3386996,3817542,5879595,15063,SRX4041474,SRS3258952,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.77937,,0.38158,,0.93681,,0.49785,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Pharyngula,Embryo,Heart,Cardiovascular System
48235,SRR7119830,SRX4041473,SRS3258951,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 1dpf mut 4,GSM3131221,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 1dpf mut 4,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / ,GSM3131221,GSM3131221: Danio rerio RNAseq singleHeart 1dpf mut 4; Danio rerio; RNA Seq,GSM3131221,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131221,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,mut_1_4_NDCII_sample_0017.fastq.gz,fastq,58279623.0,778471.0,GSM3131221 r1,0:74.86,A:18649049;C:9706373;G:12497900;T:17382327;N:43974,74,,,,18649049,9706373,12497900,17382327,43974,SRX4041473,SRS3258951,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.7618,,0.36032,,0.91425,,0.50881,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Pharyngula,Embryo,Heart,Cardiovascular System
48236,SRR7119829,SRX4041472,SRS3258950,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 1dpf mut 3,GSM3131220,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 1dpf mut 3,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / ,GSM3131220,GSM3131220: Danio rerio RNAseq singleHeart 1dpf mut 3; Danio rerio; RNA Seq,GSM3131220,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131220,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,mut_1_3_NDCII_sample_0016.fastq.gz,fastq,76875810.0,1027192.0,GSM3131220 r1,0:74.84,A:25047740;C:13094049;G:17143346;T:21533451;N:57224,74,,,,25047740,13094049,17143346,21533451,57224,SRX4041472,SRS3258950,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.73765,,0.57489,,0.91297,,0.50116,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Pharyngula,Embryo,Heart,Cardiovascular System
48237,SRR7119828,SRX4041471,SRS3258949,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 1dpf mut 2,GSM3131219,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 1dpf mut 2,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / ,GSM3131219,GSM3131219: Danio rerio RNAseq singleHeart 1dpf mut 2; Danio rerio; RNA Seq,GSM3131219,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131219,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,mut_1_2_NDCII_sample_0015.fastq.gz,fastq,279841644.0,3736395.0,GSM3131219 r1,0:74.90,A:89952643;C:48371385;G:56655773;T:84653645;N:208198,74,,,,89952643,48371385,56655773,84653645,208198,SRX4041471,SRS3258949,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.83707,,0.16537,,0.8449,,0.51435,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Pharyngula,Embryo,Heart,Cardiovascular System
48238,SRR7119827,SRX4041470,SRS3258948,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 1dpf mut 1,GSM3131218,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / ,Danio rerio RNAseq singleHeart 1dpf mut 1,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2 / ,GSM3131218,GSM3131218: Danio rerio RNAseq singleHeart 1dpf mut 1; Danio rerio; RNA Seq,GSM3131218,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131218,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,mut_1_1_NDCII_sample_0014.fastq.gz,fastq,11439626.0,152750.0,GSM3131218 r1,0:74.89,A:3900812;C:1903149;G:2137242;T:3490826;N:7597,74,,,,3900812,1903149,2137242,3490826,7597,SRX4041470,SRS3258948,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.81522,,0.22036,,0.9427,,0.50565,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Pharyngula,Embryo,Heart,Cardiovascular System
48239,SRR7119826,SRX4041469,SRS3258947,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 1dpf wt 11,GSM3131217,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 1dpf wt 11,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+,GSM3131217,GSM3131217: Danio rerio RNAseq singleHeart 1dpf wt 11; Danio rerio; RNA Seq,GSM3131217,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131217,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,W_1_11_NDCII_sample_0013.fastq.gz,fastq,42251524.0,564309.0,GSM3131217 r1,0:74.87,A:13857230;C:6932231;G:9360286;T:12071859;N:29918,74,,,,13857230,6932231,9360286,12071859,29918,SRX4041469,SRS3258947,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.73137,,0.44634,,0.93196,,0.46969,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Pharyngula,Embryo,Heart,Cardiovascular System
48240,SRR7119825,SRX4041468,SRS3258946,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 1dpf wt 9,GSM3131216,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 1dpf wt 9,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+,GSM3131216,GSM3131216: Danio rerio RNAseq singleHeart 1dpf wt 9; Danio rerio; RNA Seq,GSM3131216,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131216,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,W_1_9_NDCII_sample_0010.fastq.gz,fastq,140217783.0,1872511.0,GSM3131216 r1,0:74.88,A:48060012;C:23208078;G:28722039;T:40121038;N:106616,74,,,,48060012,23208078,28722039,40121038,106616,SRX4041468,SRS3258946,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.80665,,0.32237,,0.86778,,0.52038,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Pharyngula,Embryo,Heart,Cardiovascular System
48241,SRR7119824,SRX4041467,SRS3258945,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 1dpf wt 7,GSM3131215,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 1dpf wt 7,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+,GSM3131215,GSM3131215: Danio rerio RNAseq singleHeart 1dpf wt 7; Danio rerio; RNA Seq,GSM3131215,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131215,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,W_1_7_NDCII_sample_0008.fastq.gz,fastq,23549291.0,314631.0,GSM3131215 r1,0:74.85,A:8015580;C:3998401;G:4892477;T:6623855;N:18978,74,,,,8015580,3998401,4892477,6623855,18978,SRX4041467,SRS3258945,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.71017,,0.48929,,0.94817,,0.56724,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Pharyngula,Embryo,Heart,Cardiovascular System
48242,SRR7119823,SRX4041466,SRS3258944,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 1dpf wt 6,GSM3131214,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 1dpf wt 6,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+,GSM3131214,GSM3131214: Danio rerio RNAseq singleHeart 1dpf wt 6; Danio rerio; RNA Seq,GSM3131214,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131214,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,W_1_6_NDCII_sample_0007.fastq.gz,fastq,129689911.0,1732243.0,GSM3131214 r1,0:74.87,A:40869250;C:21297938;G:30638559;T:36786070;N:98094,74,,,,40869250,21297938,30638559,36786070,98094,SRX4041466,SRS3258944,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.77101,,0.59088,,0.88824,,0.5086,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Pharyngula,Embryo,Heart,Cardiovascular System
48243,SRR7119822,SRX4041465,SRS3258943,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 1dpf wt 5,GSM3131213,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 1dpf wt 5,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+,GSM3131213,GSM3131213: Danio rerio RNAseq singleHeart 1dpf wt 5; Danio rerio; RNA Seq,GSM3131213,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131213,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,W_1_5_NDCII_sample_0006.fastq.gz,fastq,24218974.0,323441.0,GSM3131213 r1,0:74.88,A:8220059;C:3989695;G:4906493;T:7085365;N:17362,74,,,,8220059,3989695,4906493,7085365,17362,SRX4041465,SRS3258943,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.76586,,0.49207,,0.93501,,0.55288,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Pharyngula,Embryo,Heart,Cardiovascular System
48244,SRR7119821,SRX4041464,SRS3258942,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 1dpf wt 4,GSM3131212,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 1dpf wt 4,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+,GSM3131212,GSM3131212: Danio rerio RNAseq singleHeart 1dpf wt 4; Danio rerio; RNA Seq,GSM3131212,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131212,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,W_1_4_NDCII_sample_0005.fastq.gz,fastq,22001311.0,293804.0,GSM3131212 r1,0:74.88,A:7350666;C:3795843;G:4584903;T:6252967;N:16932,74,,,,7350666,3795843,4584903,6252967,16932,SRX4041464,SRS3258942,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.7875,,0.22891,,0.93835,,0.52263,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Pharyngula,Embryo,Heart,Cardiovascular System
48245,SRR7119820,SRX4041463,SRS3258941,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 1dpf wt 3,GSM3131211,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 1dpf wt 3,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+,GSM3131211,GSM3131211: Danio rerio RNAseq singleHeart 1dpf wt 3; Danio rerio; RNA Seq,GSM3131211,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131211,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,W_1_3_NDCII_sample_0004.fastq.gz,fastq,113079916.0,1510783.0,GSM3131211 r1,0:74.85,A:37699535;C:19622685;G:23847263;T:31822581;N:87852,74,,,,37699535,19622685,23847263,31822581,87852,SRX4041463,SRS3258941,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.76704,,0.49567,,0.89045,,0.51015,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Pharyngula,Embryo,Heart,Cardiovascular System
48246,SRR7119819,SRX4041462,SRS3258977,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 1dpf wt 2,GSM3131210,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 1dpf wt 2,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+,GSM3131210,GSM3131210: Danio rerio RNAseq singleHeart 1dpf wt 2; Danio rerio; RNA Seq,GSM3131210,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131210,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,W_1_2_NDCII_sample_0003.fastq.gz,fastq,28758160.0,384087.0,GSM3131210 r1,0:74.87,A:9200574;C:4647591;G:6808365;T:8081607;N:20023,74,,,,9200574,4647591,6808365,8081607,20023,SRX4041462,SRS3258977,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.749,,0.43154,,0.92498,,0.50112,,74,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Pharyngula,Embryo,Heart,Cardiovascular System
48247,SRR7119818,SRX4041461,SRS3258961,SRP144601,PRJNA459724,The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis,GSE114038,Other,Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively,,pubmed:30867528,,Danio rerio RNAseq singleHeart 1dpf wt 1,GSM3131209,,tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+,Danio rerio RNAseq singleHeart 1dpf wt 1,RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format,heart,,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,Zebrafish Danio rerio  were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.,strain:TU/TLF mixed background|cell type:heart|age:1 dpf|genotype:myl7:GFP rnf2+/+,GSM3131209,GSM3131209: Danio rerio RNAseq singleHeart 1dpf wt 1; Danio rerio; RNA Seq,GSM3131209,,1,RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation,GEO Accession:GSM3131209,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP144601,,,W_1_1_NDCII_sample_0002.fastq.gz,fastq,115972945.0,1548390.0,GSM3131209 r1,0:74.90,A:39437412;C:19997472;G:22424748;T:34023469;N:89844,74,,,,39437412,19997472,22424748,34023469,89844,SRX4041461,SRS3258961,SRA699717,GEO,"Molecular Biology, Radboud University",1,0.81745,,0.22051,,0.87746,,0.55768,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,sc,single_cell_plate,celseq,,Netherlands,2018-05-04,Pharyngula,Embryo,Heart,Cardiovascular System
55365,SRR10321288,SRX7032108,SRS5552214,SRP226527,PRJNA578764,Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.,GSE139218,Transcriptome Analysis,While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.,,pubmed:31868166,,FK2,GSM4134187,,source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,FK2,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.",Tgnppa:mCitrine ventricle 7dpi,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,GSM4134187,GSM4134187: FK2; Danio rerio; RNA Seq,GSM4134187,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM4134187,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,Fk-2_H3MHFBGXY_S4_L001_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L001_R2_001.fastq.gz,fastq fastq,2747645940.0,18195462.0,GSM4134187 r1,0:75.51 1:75.50,A:761850296;C:390951746;G:422952266;T:1169751842;N:2139790,75,75,,,761850296,390951746,422952266,1169751842,2139790,SRX7032108,SRS5552214,SRA982819,GEO,"Bakkers, Hubrecht Institute",2,0.23534,0.89135,0.19366,0.15359,0.99902,0.86636,0.40119,0.71094,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2019-10-21,Multi-stage,Multi-stage,Heart,Cardiovascular System
55366,SRR10321289,SRX7032108,SRS5552214,SRP226527,PRJNA578764,Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.,GSE139218,Transcriptome Analysis,While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.,,pubmed:31868166,,FK2,GSM4134187,,source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,FK2,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.",Tgnppa:mCitrine ventricle 7dpi,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,GSM4134187,GSM4134187: FK2; Danio rerio; RNA Seq,GSM4134187,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM4134187,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,Fk-2_H3MHFBGXY_S4_L002_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L002_R2_001.fastq.gz,fastq fastq,2719577388.0,18010558.0,GSM4134187 r2,0:75.50 1:75.50,A:750500832;C:383761329;G:435629268;T:1147504474;N:2181485,75,75,,,750500832,383761329,435629268,1147504474,2181485,SRX7032108,SRS5552214,SRA982819,GEO,"Bakkers, Hubrecht Institute",2,0.21913,0.88799,0.16554,0.15559,0.99855,0.8704,0.48175,0.71083,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2019-10-21,Multi-stage,Multi-stage,Heart,Cardiovascular System
55367,SRR10321290,SRX7032108,SRS5552214,SRP226527,PRJNA578764,Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.,GSE139218,Transcriptome Analysis,While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.,,pubmed:31868166,,FK2,GSM4134187,,source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,FK2,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.",Tgnppa:mCitrine ventricle 7dpi,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,GSM4134187,GSM4134187: FK2; Danio rerio; RNA Seq,GSM4134187,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM4134187,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,Fk-2_H3MHFBGXY_S4_L003_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L003_R2_001.fastq.gz,fastq fastq,2396848795.0,15867573.0,GSM4134187 r3,0:75.56 1:75.50,A:649358056;C:340829352;G:366620430;T:1039511314;N:529643,75,75,,,649358056,340829352,366620430,1039511314,529643,SRX7032108,SRS5552214,SRA982819,GEO,"Bakkers, Hubrecht Institute",2,0.22581,0.89171,0.18682,0.15894,0.99928,0.87054,0.41592,0.70495,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2019-10-21,Multi-stage,Multi-stage,Heart,Cardiovascular System
55368,SRR10321291,SRX7032108,SRS5552214,SRP226527,PRJNA578764,Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.,GSE139218,Transcriptome Analysis,While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.,,pubmed:31868166,,FK2,GSM4134187,,source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,FK2,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.",Tgnppa:mCitrine ventricle 7dpi,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,GSM4134187,GSM4134187: FK2; Danio rerio; RNA Seq,GSM4134187,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM4134187,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,Fk-2_H3MHFBGXY_S4_L004_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L004_R2_001.fastq.gz,fastq fastq,2610671390.0,17282452.0,GSM4134187 r4,0:75.56 1:75.50,A:691899084;C:368646569;G:415634004;T:1133907995;N:583738,75,75,,,691899084,368646569,415634004,1133907995,583738,SRX7032108,SRS5552214,SRA982819,GEO,"Bakkers, Hubrecht Institute",2,0.24107,0.8886,0.19934,0.15491,0.99926,0.8702,0.31578,0.66998,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2019-10-21,Multi-stage,Multi-stage,Heart,Cardiovascular System
55369,SRR10321284,SRX7032107,SRS5552213,SRP226527,PRJNA578764,Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.,GSE139218,Transcriptome Analysis,While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.,,pubmed:31868166,,FK1,GSM4134186,,source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,FK1,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.",Tgnppa:mCitrine ventricle 7dpi,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,GSM4134186,GSM4134186: FK1; Danio rerio; RNA Seq,GSM4134186,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM4134186,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,FK-1_H3MHFBGXY_S3_L001_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L001_R2_001.fastq.gz,fastq fastq,2366670719.0,15672127.0,GSM4134186 r1,0:75.50 1:75.51,A:648000254;C:343663478;G:358343004;T:1014831853;N:1832130,75,75,,,648000254,343663478,358343004,1014831853,1832130,SRX7032107,SRS5552213,SRA982819,GEO,"Bakkers, Hubrecht Institute",2,0.30353,0.90485,0.25842,0.14878,0.99912,0.85857,0.23863,0.71645,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2019-10-21,Multi-stage,Multi-stage,Heart,Cardiovascular System
55370,SRR10321285,SRX7032107,SRS5552213,SRP226527,PRJNA578764,Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.,GSE139218,Transcriptome Analysis,While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.,,pubmed:31868166,,FK1,GSM4134186,,source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,FK1,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.",Tgnppa:mCitrine ventricle 7dpi,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,GSM4134186,GSM4134186: FK1; Danio rerio; RNA Seq,GSM4134186,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM4134186,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,FK-1_H3MHFBGXY_S3_L002_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L002_R2_001.fastq.gz,fastq fastq,2360571906.0,15632617.0,GSM4134186 r2,0:75.49 1:75.51,A:643644738;C:339965378;G:371359828;T:1003716606;N:1885356,75,75,,,643644738,339965378,371359828,1003716606,1885356,SRX7032107,SRS5552213,SRA982819,GEO,"Bakkers, Hubrecht Institute",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2019-10-21,Multi-stage,Multi-stage,Heart,Cardiovascular System
55371,SRR10321286,SRX7032107,SRS5552213,SRP226527,PRJNA578764,Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.,GSE139218,Transcriptome Analysis,While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.,,pubmed:31868166,,FK1,GSM4134186,,source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,FK1,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.",Tgnppa:mCitrine ventricle 7dpi,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,GSM4134186,GSM4134186: FK1; Danio rerio; RNA Seq,GSM4134186,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM4134186,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,FK-1_H3MHFBGXY_S3_L003_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L003_R2_001.fastq.gz,fastq fastq,2074411223.0,13732357.0,GSM4134186 r3,0:75.55 1:75.51,A:554276583;C:300804770;G:312025485;T:906833457;N:470928,75,75,,,554276583,300804770,312025485,906833457,470928,SRX7032107,SRS5552213,SRA982819,GEO,"Bakkers, Hubrecht Institute",2,0.2996,0.90397,0.25521,0.15245,0.99933,0.86314,0.21969,0.69653,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2019-10-21,Multi-stage,Multi-stage,Heart,Cardiovascular System
55372,SRR10321287,SRX7032107,SRS5552213,SRP226527,PRJNA578764,Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.,GSE139218,Transcriptome Analysis,While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.,,pubmed:31868166,,FK1,GSM4134186,,source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,FK1,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.",Tgnppa:mCitrine ventricle 7dpi,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,GSM4134186,GSM4134186: FK1; Danio rerio; RNA Seq,GSM4134186,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM4134186,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,FK-1_H3MHFBGXY_S3_L004_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L004_R2_001.fastq.gz,fastq fastq,2267459781.0,15009993.0,GSM4134186 r4,0:75.55 1:75.51,A:592957170;C:326713096;G:354670327;T:992614149;N:505039,75,75,,,592957170,326713096,354670327,992614149,505039,SRX7032107,SRS5552213,SRA982819,GEO,"Bakkers, Hubrecht Institute",2,0.3137,0.9006,0.26295,0.14953,0.99914,0.8622,0.19895,0.70141,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2019-10-21,Multi-stage,Multi-stage,Heart,Cardiovascular System
59985,SRR12083057,SRX8610203,SRS6899881,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 012,GSM4635178,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 012,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following order: A1 to A24   B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635178,GSM4635178: HUB DB 012; Danio rerio; RNA Seq,GSM4635178,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635178,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-012_H3HCLBGXC_S4_L001_R1_001.fastq.gz HUB-DB-012_H3HCLBGXC_S4_L001_R2_001.fastq.gz,fastq fastq,623629172.0,7251502.0,GSM4635178 r1,0:26 1:60,A:152264664;C:116216632;G:110007461;T:245137012;N:3403,26,60,,,152264664,116216632,110007461,245137012,3403,SRX8610203,SRS6899881,SRA1090808,GEO,Hubrecht,2,0.10748,0.88943,0.10172,0.27473,0.9931,0.82905,0.60372,0.48618,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59986,SRR12083058,SRX8610203,SRS6899881,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 012,GSM4635178,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 012,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following order: A1 to A24   B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635178,GSM4635178: HUB DB 012; Danio rerio; RNA Seq,GSM4635178,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635178,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-012_H3HCLBGXC_S4_L002_R1_001.fastq.gz HUB-DB-012_H3HCLBGXC_S4_L002_R2_001.fastq.gz,fastq fastq,597918268.0,6952538.0,GSM4635178 r2,0:26 1:60,A:145156634;C:110841797;G:108031654;T:233885695;N:2488,26,60,,,145156634,110841797,108031654,233885695,2488,SRX8610203,SRS6899881,SRA1090808,GEO,Hubrecht,2,0.10741,0.88528,0.10165,0.27242,0.99289,0.82994,0.60407,0.47918,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59987,SRR12083059,SRX8610203,SRS6899881,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 012,GSM4635178,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 012,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following order: A1 to A24   B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635178,GSM4635178: HUB DB 012; Danio rerio; RNA Seq,GSM4635178,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635178,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-012_H3HCLBGXC_S4_L003_R1_001.fastq.gz HUB-DB-012_H3HCLBGXC_S4_L003_R2_001.fastq.gz,fastq fastq,628530140.0,7308490.0,GSM4635178 r3,0:26 1:60,A:153358630;C:117237955;G:110777080;T:247131309;N:25166,26,60,,,153358630,117237955,110777080,247131309,25166,SRX8610203,SRS6899881,SRA1090808,GEO,Hubrecht,2,0.10839,0.88927,0.10281,0.27315,0.99316,0.8284,0.62118,0.46755,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59988,SRR12083060,SRX8610203,SRS6899881,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 012,GSM4635178,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 012,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following order: A1 to A24   B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635178,GSM4635178: HUB DB 012; Danio rerio; RNA Seq,GSM4635178,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635178,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-012_H3HCLBGXC_S4_L004_R1_001.fastq.gz HUB-DB-012_H3HCLBGXC_S4_L004_R2_001.fastq.gz,fastq fastq,605801372.0,7044202.0,GSM4635178 r4,0:26 1:60,A:147072053;C:112438811;G:109075558;T:237165161;N:49789,26,60,,,147072053,112438811,109075558,237165161,49789,SRX8610203,SRS6899881,SRA1090808,GEO,Hubrecht,2,0.10729,0.88592,0.10142,0.2715,0.99318,0.83096,0.63628,0.47975,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59989,SRR12083053,SRX8610202,SRS6899880,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 011,GSM4635177,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 011,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following order: A1 to A24   B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635177,GSM4635177: HUB DB 011; Danio rerio; RNA Seq,GSM4635177,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635177,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-011_H3HCLBGXC_S3_L001_R1_001.fastq.gz HUB-DB-011_H3HCLBGXC_S3_L001_R2_001.fastq.gz,fastq fastq,634797476.0,7381366.0,GSM4635177 r1,0:26 1:60,A:153195131;C:118480864;G:115080449;T:248037462;N:3570,26,60,,,153195131,118480864,115080449,248037462,3570,SRX8610202,SRS6899880,SRA1090808,GEO,Hubrecht,2,0.11082,0.89281,0.10414,0.28784,0.99204,0.82619,0.66824,0.50609,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59990,SRR12083054,SRX8610202,SRS6899880,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 011,GSM4635177,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 011,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following order: A1 to A24   B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635177,GSM4635177: HUB DB 011; Danio rerio; RNA Seq,GSM4635177,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635177,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-011_H3HCLBGXC_S3_L002_R1_001.fastq.gz HUB-DB-011_H3HCLBGXC_S3_L002_R2_001.fastq.gz,fastq fastq,611046770.0,7105195.0,GSM4635177 r2,0:26 1:60,A:146818280;C:113612783;G:112799955;T:237813147;N:2605,26,60,,,146818280,113612783,112799955,237813147,2605,SRX8610202,SRS6899880,SRA1090808,GEO,Hubrecht,2,0.11194,0.89124,0.10494,0.28808,0.99275,0.83071,0.67141,0.50375,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59991,SRR12083055,SRX8610202,SRS6899880,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 011,GSM4635177,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 011,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following order: A1 to A24   B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635177,GSM4635177: HUB DB 011; Danio rerio; RNA Seq,GSM4635177,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635177,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-011_H3HCLBGXC_S3_L003_R1_001.fastq.gz HUB-DB-011_H3HCLBGXC_S3_L003_R2_001.fastq.gz,fastq fastq,641591132.0,7460362.0,GSM4635177 r3,0:26 1:60,A:154776835;C:119807925;G:116219737;T:250759686;N:26949,26,60,,,154776835,119807925,116219737,250759686,26949,SRX8610202,SRS6899880,SRA1090808,GEO,Hubrecht,2,0.11171,0.8947,0.10479,0.29095,0.99233,0.82775,0.69148,0.50141,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59992,SRR12083056,SRX8610202,SRS6899880,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 011,GSM4635177,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 011,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following order: A1 to A24   B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635177,GSM4635177: HUB DB 011; Danio rerio; RNA Seq,GSM4635177,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635177,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-011_H3HCLBGXC_S3_L004_R1_001.fastq.gz HUB-DB-011_H3HCLBGXC_S3_L004_R2_001.fastq.gz,fastq fastq,619988534.0,7209169.0,GSM4635177 r4,0:26 1:60,A:149057849;C:115334020;G:114131475;T:241414817;N:50373,26,60,,,149057849,115334020,114131475,241414817,50373,SRX8610202,SRS6899880,SRA1090808,GEO,Hubrecht,2,0.11255,0.89073,0.10573,0.28703,0.99283,0.83061,0.6874,0.50364,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59993,SRR12083049,SRX8610201,SRS6899879,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 010,GSM4635176,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 010,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following order: A1 to A24   B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635176,GSM4635176: HUB DB 010; Danio rerio; RNA Seq,GSM4635176,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635176,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-010_H3HCLBGXC_S2_L001_R1_001.fastq.gz HUB-DB-010_H3HCLBGXC_S2_L001_R2_001.fastq.gz,fastq fastq,673568770.0,7832195.0,GSM4635176 r1,0:26 1:60,A:164220958;C:127417067;G:127429427;T:254497649;N:3669,26,60,,,164220958,127417067,127429427,254497649,3669,SRX8610201,SRS6899879,SRA1090808,GEO,Hubrecht,2,0.10904,0.86908,0.10146,0.28252,0.99086,0.83952,0.55689,0.51097,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59994,SRR12083050,SRX8610201,SRS6899879,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 010,GSM4635176,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 010,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following order: A1 to A24   B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635176,GSM4635176: HUB DB 010; Danio rerio; RNA Seq,GSM4635176,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635176,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-010_H3HCLBGXC_S2_L002_R1_001.fastq.gz HUB-DB-010_H3HCLBGXC_S2_L002_R2_001.fastq.gz,fastq fastq,642282486.0,7468401.0,GSM4635176 r2,0:26 1:60,A:156140841;C:120979080;G:123582811;T:241577191;N:2563,26,60,,,156140841,120979080,123582811,241577191,2563,SRX8610201,SRS6899879,SRA1090808,GEO,Hubrecht,2,0.10877,0.86702,0.10115,0.2848,0.98961,0.84122,0.5621,0.48392,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59995,SRR12083051,SRX8610201,SRS6899879,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 010,GSM4635176,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 010,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following order: A1 to A24   B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635176,GSM4635176: HUB DB 010; Danio rerio; RNA Seq,GSM4635176,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635176,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-010_H3HCLBGXC_S2_L003_R1_001.fastq.gz HUB-DB-010_H3HCLBGXC_S2_L003_R2_001.fastq.gz,fastq fastq,676661932.0,7868162.0,GSM4635176 r3,0:26 1:60,A:165121933;C:128034418;G:127770885;T:255708762;N:25934,26,60,,,165121933,128034418,127770885,255708762,25934,SRX8610201,SRS6899879,SRA1090808,GEO,Hubrecht,2,0.10987,0.87058,0.103,0.282,0.99109,0.83915,0.55503,0.51595,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59996,SRR12083052,SRX8610201,SRS6899879,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 010,GSM4635176,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 010,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following order: A1 to A24   B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635176,GSM4635176: HUB DB 010; Danio rerio; RNA Seq,GSM4635176,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635176,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-010_H3HCLBGXC_S2_L004_R1_001.fastq.gz HUB-DB-010_H3HCLBGXC_S2_L004_R2_001.fastq.gz,fastq fastq,649298624.0,7549984.0,GSM4635176 r4,0:26 1:60,A:158062491;C:122309175;G:124562965;T:244314794;N:49199,26,60,,,158062491,122309175,124562965,244314794,49199,SRX8610201,SRS6899879,SRA1090808,GEO,Hubrecht,2,0.11052,0.86686,0.1033,0.2819,0.99052,0.84066,0.55805,0.50641,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59997,SRR12083045,SRX8610200,SRS6899878,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 009,GSM4635175,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 009,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following order: A1 to A24   B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635175,GSM4635175: HUB DB 009; Danio rerio; RNA Seq,GSM4635175,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635175,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-009_H3HCLBGXC_S1_L001_R1_001.fastq.gz HUB-DB-009_H3HCLBGXC_S1_L001_R2_001.fastq.gz,fastq fastq,893990210.0,10395235.0,GSM4635175 r1,0:26 1:60,A:217651633;C:169265774;G:172112042;T:334955815;N:4946,26,60,,,217651633,169265774,172112042,334955815,4946,SRX8610200,SRS6899878,SRA1090808,GEO,Hubrecht,2,0.1006,0.81888,0.09561,0.29404,0.99318,0.83806,0.67678,0.52964,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59998,SRR12083046,SRX8610200,SRS6899878,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 009,GSM4635175,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 009,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following order: A1 to A24   B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635175,GSM4635175: HUB DB 009; Danio rerio; RNA Seq,GSM4635175,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635175,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-009_H3HCLBGXC_S1_L002_R1_001.fastq.gz HUB-DB-009_H3HCLBGXC_S1_L002_R2_001.fastq.gz,fastq fastq,859084960.0,9989360.0,GSM4635175 r2,0:26 1:60,A:208058112;C:161872788;G:168851400;T:320298922;N:3738,26,60,,,208058112,161872788,168851400,320298922,3738,SRX8610200,SRS6899878,SRA1090808,GEO,Hubrecht,2,0.10183,0.81219,0.09621,0.29163,0.99281,0.83755,0.65329,0.52165,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59999,SRR12083047,SRX8610200,SRS6899878,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 009,GSM4635175,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 009,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following order: A1 to A24   B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635175,GSM4635175: HUB DB 009; Danio rerio; RNA Seq,GSM4635175,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635175,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-009_H3HCLBGXC_S1_L003_R1_001.fastq.gz HUB-DB-009_H3HCLBGXC_S1_L003_R2_001.fastq.gz,fastq fastq,903479192.0,10505572.0,GSM4635175 r3,0:26 1:60,A:220083458;C:171123276;G:173673810;T:338562517;N:36131,26,60,,,220083458,171123276,173673810,338562517,36131,SRX8610200,SRS6899878,SRA1090808,GEO,Hubrecht,2,0.10152,0.81676,0.09602,0.29263,0.99255,0.83717,0.63699,0.5171,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
60000,SRR12083048,SRX8610200,SRS6899878,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 009,GSM4635175,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 009,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following order: A1 to A24   B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635175,GSM4635175: HUB DB 009; Danio rerio; RNA Seq,GSM4635175,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635175,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-009_H3HCLBGXC_S1_L004_R1_001.fastq.gz HUB-DB-009_H3HCLBGXC_S1_L004_R2_001.fastq.gz,fastq fastq,872389848.0,10144068.0,GSM4635175 r4,0:26 1:60,A:211449890;C:164472082;G:170979230;T:325419371;N:69275,26,60,,,211449890,164472082,170979230,325419371,69275,SRX8610200,SRS6899878,SRA1090808,GEO,Hubrecht,2,0.10082,0.81569,0.09542,0.29303,0.99226,0.84033,0.65927,0.52879,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
62867,SRR13426641,SRX9841732,SRS8023820,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 005,GSM5017826,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 005,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017826,GSM5017826: HUB DB 005; Danio rerio; RNA Seq,GSM5017826,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017826,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,HUB-DB-005_HNWVVBGX9_S4_L001_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L001_R2_001.fastq.gz,fastq fastq,806178534.0,9374169.0,GSM5017826 r1,0:26 1:60,A:213590554;C:148614157;G:163804315;T:279996916;N:172592,26,60,,,213590554,148614157,163804315,279996916,172592,SRX9841732,SRS8023820,SRA1183369,GEO,FLI,2,0.10779,0.7922,0.10106,0.39356,0.99281,0.93701,0.66257,0.39639,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62868,SRR13426642,SRX9841732,SRS8023820,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 005,GSM5017826,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 005,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017826,GSM5017826: HUB DB 005; Danio rerio; RNA Seq,GSM5017826,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017826,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,HUB-DB-005_HNWVVBGX9_S4_L002_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L002_R2_001.fastq.gz,fastq fastq,874594286.0,10169701.0,GSM5017826 r2,0:26 1:60,A:227213153;C:160851586;G:182364146;T:303951184;N:214217,26,60,,,227213153,160851586,182364146,303951184,214217,SRX9841732,SRS8023820,SRA1183369,GEO,FLI,2,0.11067,0.8032,0.10412,0.40169,0.9931,0.93332,0.65468,0.40908,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62869,SRR13426643,SRX9841732,SRS8023820,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 005,GSM5017826,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 005,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017826,GSM5017826: HUB DB 005; Danio rerio; RNA Seq,GSM5017826,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017826,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,HUB-DB-005_HNWVVBGX9_S4_L003_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L003_R2_001.fastq.gz,fastq fastq,831835860.0,9672510.0,GSM5017826 r3,0:26 1:60,A:220300204;C:153061412;G:168938657;T:289375449;N:160138,26,60,,,220300204,153061412,168938657,289375449,160138,SRX9841732,SRS8023820,SRA1183369,GEO,FLI,2,0.10982,0.78672,0.10334,0.39196,0.99297,0.93675,0.64735,0.36252,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62870,SRR13426644,SRX9841732,SRS8023820,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 005,GSM5017826,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 005,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017826,GSM5017826: HUB DB 005; Danio rerio; RNA Seq,GSM5017826,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017826,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,HUB-DB-005_HNWVVBGX9_S4_L004_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L004_R2_001.fastq.gz,fastq fastq,692573136.0,8053176.0,GSM5017826 r4,0:26 1:60,A:182418113;C:126757471;G:143869511;T:239393143;N:134898,26,60,,,182418113,126757471,143869511,239393143,134898,SRX9841732,SRS8023820,SRA1183369,GEO,FLI,2,0.10828,0.81367,0.10186,0.40356,0.99316,0.94018,0.65073,0.40086,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62871,SRR13426637,SRX9841731,SRS8023819,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 001,GSM5017825,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 001,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017825,GSM5017825: HUB DB 001; Danio rerio; RNA Seq,GSM5017825,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017825,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,HUB-DB-001_AHVKTGBGX7_S5_L001_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L001_R2_001.fastq.gz,fastq fastq,471703034.0,5484919.0,GSM5017825 r1,0:26 1:60,A:125045012;C:89627491;G:85413855;T:171466861;N:149815,26,60,,,125045012,89627491,85413855,171466861,149815,SRX9841731,SRS8023819,SRA1183369,GEO,FLI,2,0.10907,0.67995,0.10221,0.30484,0.99127,0.94229,0.63864,0.4574,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62872,SRR13426638,SRX9841731,SRS8023819,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 001,GSM5017825,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 001,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017825,GSM5017825: HUB DB 001; Danio rerio; RNA Seq,GSM5017825,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017825,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,HUB-DB-001_AHVKTGBGX7_S5_L002_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L002_R2_001.fastq.gz,fastq fastq,489372938.0,5690383.0,GSM5017825 r2,0:26 1:60,A:131516821;C:92202683;G:88685608;T:176824985;N:142841,26,60,,,131516821,92202683,88685608,176824985,142841,SRX9841731,SRS8023819,SRA1183369,GEO,FLI,2,0.11044,0.6808,0.10316,0.30432,0.99121,0.94868,0.59663,0.46502,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62873,SRR13426639,SRX9841731,SRS8023819,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 001,GSM5017825,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 001,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017825,GSM5017825: HUB DB 001; Danio rerio; RNA Seq,GSM5017825,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017825,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,HUB-DB-001_AHVKTGBGX7_S5_L003_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L003_R2_001.fastq.gz,fastq fastq,407735288.0,4741108.0,GSM5017825 r3,0:26 1:60,A:108841476;C:77418215;G:73171345;T:148203998;N:100254,26,60,,,108841476,77418215,73171345,148203998,100254,SRX9841731,SRS8023819,SRA1183369,GEO,FLI,2,0.10885,0.6707,0.10183,0.29574,0.99137,0.94702,0.66157,0.42386,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62874,SRR13426640,SRX9841731,SRS8023819,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 001,GSM5017825,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 001,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017825,GSM5017825: HUB DB 001; Danio rerio; RNA Seq,GSM5017825,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017825,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,HUB-DB-001_AHVKTGBGX7_S5_L004_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L004_R2_001.fastq.gz,fastq fastq,505539304.0,5878364.0,GSM5017825 r4,0:26 1:60,A:135189083;C:94908231;G:92431583;T:182885125;N:125282,26,60,,,135189083,94908231,92431583,182885125,125282,SRX9841731,SRS8023819,SRA1183369,GEO,FLI,2,0.10991,0.68593,0.10302,0.30489,0.99135,0.94799,0.66557,0.42206,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62875,SRR13426633,SRX9841730,SRS8023818,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 008,GSM5017831,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 008,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017831,GSM5017831: HUB DB 008; Danio rerio; RNA Seq,GSM5017831,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017831,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,HUB-DB-008_HNWVVBGX9_S7_L001_R1_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L001_R2_001.fastq.gz,fastq fastq,529790530.0,6160355.0,GSM5017831 r1,0:26 1:60,A:134254092;C:100685793;G:108463112;T:186279563;N:107970,26,60,,,134254092,100685793,108463112,186279563,107970,SRX9841730,SRS8023818,SRA1183369,GEO,FLI,2,0.11279,0.80911,0.10456,0.43276,0.99127,0.93927,0.65164,0.5415,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62876,SRR13426634,SRX9841730,SRS8023818,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 008,GSM5017831,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 008,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017831,GSM5017831: HUB DB 008; Danio rerio; RNA Seq,GSM5017831,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017831,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,HUB-DB-008_HNWVVBGX9_S7_L002_R1_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L002_R2_001.fastq.gz,fastq fastq,611015122.0,7104827.0,GSM5017831 r2,0:26 1:60,A:152137832;C:116026517;G:127735448;T:214967198;N:148127,26,60,,,152137832,116026517,127735448,214967198,148127,SRX9841730,SRS8023818,SRA1183369,GEO,FLI,2,0.11412,0.81784,0.1057,0.44203,0.99151,0.93421,0.59611,0.54448,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62877,SRR13426635,SRX9841730,SRS8023818,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 008,GSM5017831,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 008,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017831,GSM5017831: HUB DB 008; Danio rerio; RNA Seq,GSM5017831,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017831,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,HUB-DB-008_HNWVVBGX9_S7_L003_R1_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L003_R2_001.fastq.gz,fastq fastq,554981822.0,6453277.0,GSM5017831 r3,0:26 1:60,A:140664360;C:105281601;G:113575873;T:195359632;N:100356,26,60,,,140664360,105281601,113575873,195359632,100356,SRX9841730,SRS8023818,SRA1183369,GEO,FLI,2,0.11356,0.80646,0.10543,0.42991,0.99125,0.93996,0.67419,0.52863,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62878,SRR13426636,SRX9841730,SRS8023818,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 008,GSM5017831,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 008,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017831,GSM5017831: HUB DB 008; Danio rerio; RNA Seq,GSM5017831,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017831,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,HUB-DB-008_HNWVVBGX9_S7_L004_R1_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L004_R2_001.fastq.gz,fastq fastq,459861436.0,5347226.0,GSM5017831 r4,0:26 1:60,A:115949245;C:86913961;G:95720860;T:161187969;N:89401,26,60,,,115949245,86913961,95720860,161187969,89401,SRX9841730,SRS8023818,SRA1183369,GEO,FLI,2,0.11252,0.81111,0.10402,0.43407,0.99149,0.9403,0.64627,0.53769,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62879,SRR13426629,SRX9841729,SRS8023817,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 007,GSM5017830,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 007,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017830,GSM5017830: HUB DB 007; Danio rerio; RNA Seq,GSM5017830,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017830,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,HUB-DB-007_HNWVVBGX9_S6_L001_R1_001.fastq.gz HUB-DB-007_HNWVVBGX9_S6_L001_R2_001.fastq.gz,fastq fastq,584059454.0,6791389.0,GSM5017830 r1,0:26 1:60,A:162038298;C:107975394;G:118251259;T:195669218;N:125285,26,60,,,162038298,107975394,118251259,195669218,125285,SRX9841729,SRS8023817,SRA1183369,GEO,FLI,2,0.08872,0.68675,0.08343,0.37824,0.99344,0.94957,0.6145,0.42826,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System