run_metadata
176 rows where experiment.library_strategy = "RNA-Seq", technology = "celseq" and tissue_curation = "Heart"
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| Link | 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 |
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| 25228 | 25228 | SRR25685572 | SRX21410761 | SRS18649243 | SRP455780 | PRJNA1006660 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish] | GSE241156 | Other | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | zebrafish 14dpi heart3 | GSM7717530 | source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi|geo loc name:missing|collection date:missing | zebrafish 14dpi heart3 | Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. 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 Assembly: GRCm38 for mouse danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish | adult heart | Unfixed hearts were isolated and tissue was cut out 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:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi | GSM7717530 | GSM7717530: zebrafish 14dpi heart3; Danio rerio; RNA Seq | GSM7717530 r1 | GSM7717530 | 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 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP455780 | loader:fastq load.py|options: allowEarlyFileEnd | DB14zf4_R1.fq DB14zf4_R2.fq | fastq fastq | 571157496.0 | 7312520.0 | GSM7717530 r1 | A:132329616;C:53169305;G:72431948;T:313058610;N:168017 | 132329616 | 53169305 | 72431948 | 313058610 | 168017 | SRX21410761 | SRS18649243 | SRA1751823 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.01414 | 0.679 | 0.01413 | 0.08289 | 1.0 | 0.98395 | 0.48915 | 76 | 76 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | celseq | Netherlands | 2023-08-18 | Adult | Adult | Heart | Cardiovascular System | |||||||||||||
| 25229 | 25229 | SRR25685573 | SRX21410760 | SRS18649241 | SRP455780 | PRJNA1006660 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish] | GSE241156 | Other | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | zebrafish 14dpi heart2 | GSM7717529 | source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi|geo loc name:missing|collection date:missing | zebrafish 14dpi heart2 | Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. 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 Assembly: GRCm38 for mouse danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish | adult heart | Unfixed hearts were isolated and tissue was cut out 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:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi | GSM7717529 | GSM7717529: zebrafish 14dpi heart2; Danio rerio; RNA Seq | GSM7717529 r1 | GSM7717529 | 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 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP455780 | loader:fastq load.py|options: allowEarlyFileEnd | DB14zf3_R1.fq DB14zf3_R2.fq | fastq fastq | 97890367.0 | 1292037.0 | GSM7717529 r1 | A:21637243;C:8563955;G:12004508;T:55662880;N:21781 | 21637243 | 8563955 | 12004508 | 55662880 | 21781 | SRX21410760 | SRS18649241 | SRA1751823 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.0 | 0.689 | 0.0 | 0.07655 | 1.0 | 0.99831 | 0.63709 | 76 | 75 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | celseq | Netherlands | 2023-08-18 | Adult | Adult | Heart | Cardiovascular System | |||||||||||||
| 25230 | 25230 | SRR25685574 | SRX21410759 | SRS18649242 | SRP455780 | PRJNA1006660 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish] | GSE241156 | Other | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | zebrafish 14dpi heart1 | GSM7717528 | source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi|geo loc name:missing|collection date:missing | zebrafish 14dpi heart1 | Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. 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 Assembly: GRCm38 for mouse danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish | adult heart | Unfixed hearts were isolated and tissue was cut out 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:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi | GSM7717528 | GSM7717528: zebrafish 14dpi heart1; Danio rerio; RNA Seq | GSM7717528 r1 | GSM7717528 | 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 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP455780 | loader:fastq load.py|options: allowEarlyFileEnd | DB14zf1_R1.fq DB14zf1_R2.fq | fastq fastq | 1031757474.0 | 7257847.0 | GSM7717528 r1 | A:276216587;C:146620316;G:184052670;T:423474577;N:1393324 | 276216587 | 146620316 | 184052670 | 423474577 | 1393324 | SRX21410759 | SRS18649242 | SRA1751823 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.04176 | 0.6198 | 0.03023 | 0.08234 | 0.99894 | 0.88885 | 0.64556 | 0.53126 | 76 | 75 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | celseq | Netherlands | 2023-08-18 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 25231 | 25231 | SRR25685575 | SRX21410758 | SRS18649240 | SRP455780 | PRJNA1006660 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish] | GSE241156 | Other | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | zebrafish 7dpi heart3 | GSM7717527 | source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi|geo loc name:missing|collection date:missing | zebrafish 7dpi heart3 | Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. 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 Assembly: GRCm38 for mouse danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish | adult heart | Unfixed hearts were isolated and tissue was cut out 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:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi | GSM7717527 | GSM7717527: zebrafish 7dpi heart3; Danio rerio; RNA Seq | GSM7717527 r1 | GSM7717527 | 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 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP455780 | loader:fastq load.py|options: allowEarlyFileEnd | D37DPIZF3_R1.fq D37DPIZF3_R2.fq | fastq fastq | 898901460.0 | 7585924.0 | GSM7717527 r1 | A:236935836;C:100995680;G:128458892;T:431620821;N:890231 | 236935836 | 100995680 | 128458892 | 431620821 | 890231 | SRX21410758 | SRS18649240 | SRA1751823 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.12082 | 0.70068 | 0.10594 | 0.1234 | 0.99983 | 0.90136 | 0.875 | 0.48346 | 75 | 76 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | celseq | Netherlands | 2023-08-18 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 25232 | 25232 | SRR25685576 | SRX21410757 | SRS18649239 | SRP455780 | PRJNA1006660 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish] | GSE241156 | Other | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | zebrafish 7dpi heart2 | GSM7717526 | source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi|geo loc name:missing|collection date:missing | zebrafish 7dpi heart2 | Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. 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 Assembly: GRCm38 for mouse danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish | adult heart | Unfixed hearts were isolated and tissue was cut out 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:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi | GSM7717526 | GSM7717526: zebrafish 7dpi heart2; Danio rerio; RNA Seq | GSM7717526 r1 | GSM7717526 | 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 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP455780 | loader:fastq load.py|options: allowEarlyFileEnd | D27DPIZF2_R1.fq D27DPIZF2_R2.fq | fastq fastq | 1060429257.0 | 7609110.0 | GSM7717526 r1 | A:283107752;C:130181128;G:159305328;T:486464477;N:1370572 | 283107752 | 130181128 | 159305328 | 486464477 | 1370572 | SRX21410757 | SRS18649239 | SRA1751823 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.19472 | 0.68783 | 0.17584 | 0.16739 | 0.99967 | 0.85628 | 0.44 | 0.56319 | 75 | 76 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | celseq | Netherlands | 2023-08-18 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 25233 | 25233 | SRR25685577 | SRX21410756 | SRS18649238 | SRP455780 | PRJNA1006660 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish] | GSE241156 | Other | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | zebrafish 7dpi heart1 | GSM7717525 | source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi|geo loc name:missing|collection date:missing | zebrafish 7dpi heart1 | Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. 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 Assembly: GRCm38 for mouse danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish | adult heart | Unfixed hearts were isolated and tissue was cut out 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:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi | GSM7717525 | GSM7717525: zebrafish 7dpi heart1; Danio rerio; RNA Seq | GSM7717525 r1 | GSM7717525 | 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 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP455780 | loader:fastq load.py|options: allowEarlyFileEnd | D17DPIZF1_R1.fq D17DPIZF1_R2.fq | fastq fastq | 1073044507.0 | 7624815.0 | GSM7717525 r1 | A:288576038;C:136858647;G:170330711;T:475869519;N:1409592 | 288576038 | 136858647 | 170330711 | 475869519 | 1409592 | SRX21410756 | SRS18649238 | SRA1751823 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.15938 | 0.70435 | 0.14583 | 0.08079 | 0.99981 | 0.87949 | 0.38461 | 0.57027 | 75 | 76 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | celseq | Netherlands | 2023-08-18 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||
| 25234 | 25234 | SRR25685578 | SRX21410755 | SRS18649237 | SRP455780 | PRJNA1006660 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish] | GSE241156 | Other | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | zebrafish 3dpi heart3 | GSM7717524 | source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi|geo loc name:missing|collection date:missing | zebrafish 3dpi heart3 | Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. 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 Assembly: GRCm38 for mouse danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish | adult heart | Unfixed hearts were isolated and tissue was cut out 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:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi | GSM7717524 | GSM7717524: zebrafish 3dpi heart3; Danio rerio; RNA Seq | GSM7717524 r1 | GSM7717524 | 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 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP455780 | FKHEART3_R1.fastq FKHEART3_R2.fastq | fastq fastq | 781079621.0 | 5184230.0 | GSM7717524 r1 | 0:75.26 1:75.40 | A:277491111;C:118539142;G:116911958;T:268048500;N:88910 | 75 | 75 | 277491111 | 118539142 | 116911958 | 268048500 | 88910 | SRX21410755 | SRS18649237 | SRA1751823 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.04348 | 0.71869 | 0.04347 | 0.28823 | 1.0 | 0.79681 | 0.53909 | 76 | 75 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | celseq | Netherlands | 2023-08-18 | Adult | Adult | Heart | Cardiovascular System | |||||||||||
| 25235 | 25235 | SRR25685579 | SRX21410754 | SRS18649236 | SRP455780 | PRJNA1006660 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish] | GSE241156 | Other | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | zebrafish 3dpi heart2 | GSM7717523 | source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi|geo loc name:missing|collection date:missing | zebrafish 3dpi heart2 | Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. 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 Assembly: GRCm38 for mouse danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish | adult heart | Unfixed hearts were isolated and tissue was cut out 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:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi | GSM7717523 | GSM7717523: zebrafish 3dpi heart2; Danio rerio; RNA Seq | GSM7717523 r1 | GSM7717523 | 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 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP455780 | FKHEART2_R1.fastq FKHEART2_R2.fastq | fastq fastq | 684820059.0 | 4547520.0 | GSM7717523 r1 | 0:75.21 1:75.38 | A:258487418;C:93776953;G:97187917;T:235293267;N:74504 | 75 | 75 | 258487418 | 93776953 | 97187917 | 235293267 | 74504 | SRX21410754 | SRS18649236 | SRA1751823 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.09406 | 0.79542 | 0.09405 | 0.0802 | 1.0 | 0.83029 | 0.56367 | 75 | 75 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | celseq | Netherlands | 2023-08-18 | Adult | Adult | Heart | Cardiovascular System | |||||||||||
| 25236 | 25236 | SRR25685580 | SRX21410753 | SRS18649235 | SRP455780 | PRJNA1006660 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish] | GSE241156 | Other | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | zebrafish 3dpi heart1 | GSM7717522 | source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi|geo loc name:missing|collection date:missing | zebrafish 3dpi heart1 | Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. 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 Assembly: GRCm38 for mouse danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish | adult heart | Unfixed hearts were isolated and tissue was cut out 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:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi | GSM7717522 | GSM7717522: zebrafish 3dpi heart1; Danio rerio; RNA Seq | GSM7717522 r1 | GSM7717522 | 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 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP455780 | FKHEART1_R1.fastq FKHEART1_R2.fastq | fastq fastq | 784558404.0 | 5209213.0 | GSM7717522 r1 | 0:75.22 1:75.39 | A:291009319;C:102718146;G:111606154;T:279144074;N:80711 | 75 | 75 | 291009319 | 102718146 | 111606154 | 279144074 | 80711 | SRX21410753 | SRS18649235 | SRA1751823 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.13119 | 0.82035 | 0.12871 | 0.08445 | 0.99997 | 0.82785 | 0.0 | 0.56254 | 76 | 76 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | celseq | Netherlands | 2023-08-18 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25239 | 25239 | SRR25723792 | SRX21447930 | SRS18684553 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | hmga1a mutant plate 4 | GSM7728123 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | hmga1a mutant plate 4 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728123 | GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq | GSM7728123 r1 | GSM7728123 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | HUB-DB-008_HNWVVBGX9_S7_L001_R2_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L001_R1_001.fastq.gz | fastq fastq | 529790530.0 | 6160355.0 | GSM7728123 r1 | 0:26 1:60 | A:134254092;C:100685793;G:108463112;T:186279563;N:107970 | 26 | 60 | 134254092 | 100685793 | 108463112 | 186279563 | 107970 | SRX21447930 | SRS18684553 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.11277 | 0.80912 | 0.10457 | 0.43275 | 0.99131 | 0.93933 | 0.67026 | 0.54274 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25240 | 25240 | SRR25723793 | SRX21447930 | SRS18684553 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | hmga1a mutant plate 4 | GSM7728123 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | hmga1a mutant plate 4 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728123 | GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq | GSM7728123 r1 | GSM7728123 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | 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 | GSM7728123 r2 | 0:26 1:60 | A:152137832;C:116026517;G:127735448;T:214967198;N:148127 | 26 | 60 | 152137832 | 116026517 | 127735448 | 214967198 | 148127 | SRX21447930 | SRS18684553 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.11413 | 0.81785 | 0.10565 | 0.44205 | 0.99119 | 0.93419 | 0.59743 | 0.53882 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25241 | 25241 | SRR25723794 | SRX21447930 | SRS18684553 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | hmga1a mutant plate 4 | GSM7728123 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | hmga1a mutant plate 4 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728123 | GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq | GSM7728123 r1 | GSM7728123 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | HUB-DB-008_HNWVVBGX9_S7_L003_R2_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L003_R1_001.fastq.gz | fastq fastq | 554981822.0 | 6453277.0 | GSM7728123 r3 | 0:26 1:60 | A:140664360;C:105281601;G:113575873;T:195359632;N:100356 | 26 | 60 | 140664360 | 105281601 | 113575873 | 195359632 | 100356 | SRX21447930 | SRS18684553 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.11352 | 0.80651 | 0.10538 | 0.42971 | 0.99137 | 0.93994 | 0.65893 | 0.53098 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25242 | 25242 | SRR25723795 | SRX21447930 | SRS18684553 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | hmga1a mutant plate 4 | GSM7728123 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | hmga1a mutant plate 4 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728123 | GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq | GSM7728123 r1 | GSM7728123 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | HUB-DB-008_HNWVVBGX9_S7_L004_R2_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L004_R1_001.fastq.gz | fastq fastq | 459861436.0 | 5347226.0 | GSM7728123 r4 | 0:26 1:60 | A:115949245;C:86913961;G:95720860;T:161187969;N:89401 | 26 | 60 | 115949245 | 86913961 | 95720860 | 161187969 | 89401 | SRX21447930 | SRS18684553 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.11249 | 0.81109 | 0.10407 | 0.43334 | 0.99135 | 0.94034 | 0.64852 | 0.53864 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25243 | 25243 | SRR25723796 | SRX21447929 | SRS18684552 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | hmga1a mutant plate 3 | GSM7728122 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | hmga1a mutant plate 3 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728122 | GSM7728122: hmga1a mutant plate 3; Danio rerio; RNA Seq | GSM7728122 r1 | GSM7728122 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | 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 | GSM7728122 r1 | 0:26 1:60 | A:162038298;C:107975394;G:118251259;T:195669218;N:125285 | 26 | 60 | 162038298 | 107975394 | 118251259 | 195669218 | 125285 | SRX21447929 | SRS18684552 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.08872 | 0.68673 | 0.08328 | 0.37858 | 0.99346 | 0.94945 | 0.60282 | 0.42608 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25244 | 25244 | SRR25723797 | SRX21447929 | SRS18684552 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | hmga1a mutant plate 3 | GSM7728122 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | hmga1a mutant plate 3 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728122 | GSM7728122: hmga1a mutant plate 3; Danio rerio; RNA Seq | GSM7728122 r1 | GSM7728122 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | HUB-DB-007_HNWVVBGX9_S6_L002_R1_001.fastq.gz HUB-DB-007_HNWVVBGX9_S6_L002_R2_001.fastq.gz | fastq fastq | 641359448.0 | 7457668.0 | GSM7728122 r2 | 0:26 1:60 | A:174443468;C:118438230;G:132604485;T:215721538;N:151727 | 26 | 60 | 174443468 | 118438230 | 132604485 | 215721538 | 151727 | SRX21447929 | SRS18684552 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.09277 | 0.71427 | 0.08722 | 0.3942 | 0.99338 | 0.94594 | 0.56903 | 0.45872 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25245 | 25245 | SRR25723798 | SRX21447929 | SRS18684552 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | hmga1a mutant plate 3 | GSM7728122 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | hmga1a mutant plate 3 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728122 | GSM7728122: hmga1a mutant plate 3; Danio rerio; RNA Seq | GSM7728122 r1 | GSM7728122 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | HUB-DB-007_HNWVVBGX9_S6_L003_R1_001.fastq.gz HUB-DB-007_HNWVVBGX9_S6_L003_R2_001.fastq.gz | fastq fastq | 609857046.0 | 7091361.0 | GSM7728122 r3 | 0:26 1:60 | A:169007241;C:112556048;G:123345017;T:204831635;N:117105 | 26 | 60 | 169007241 | 112556048 | 123345017 | 204831635 | 117105 | SRX21447929 | SRS18684552 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.09058 | 0.68251 | 0.08521 | 0.37718 | 0.99332 | 0.95156 | 0.59403 | 0.44605 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25246 | 25246 | SRR25723799 | SRX21447929 | SRS18684552 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | hmga1a mutant plate 3 | GSM7728122 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | hmga1a mutant plate 3 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728122 | GSM7728122: hmga1a mutant plate 3; Danio rerio; RNA Seq | GSM7728122 r1 | GSM7728122 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | HUB-DB-007_HNWVVBGX9_S6_L004_R1_001.fastq.gz HUB-DB-007_HNWVVBGX9_S6_L004_R2_001.fastq.gz | fastq fastq | 514759966.0 | 5985581.0 | GSM7728122 r4 | 0:26 1:60 | A:142060859;C:94579961;G:106100208;T:171916257;N:102681 | 26 | 60 | 142060859 | 94579961 | 106100208 | 171916257 | 102681 | SRX21447929 | SRS18684552 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.08962 | 0.7176 | 0.08411 | 0.39394 | 0.99293 | 0.95189 | 0.55398 | 0.46149 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25247 | 25247 | SRR25723800 | SRX21447928 | SRS18684551 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | wildtype plate 3 | GSM7728121 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | wildtype plate 3 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728121 | GSM7728121: wildtype plate 3; Danio rerio; RNA Seq | GSM7728121 r1 | GSM7728121 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | HUB-DB-006_HNWVVBGX9_S5_L001_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L001_R2_001.fastq.gz | fastq fastq | 929999528.0 | 10813948.0 | GSM7728121 r1 | 0:26 1:60 | A:240334465;C:174255952;G:184260587;T:330943403;N:205121 | 26 | 60 | 240334465 | 174255952 | 184260587 | 330943403 | 205121 | SRX21447928 | SRS18684551 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.11113 | 0.87407 | 0.10304 | 0.43976 | 0.992 | 0.93034 | 0.63031 | 0.44624 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25248 | 25248 | SRR25723801 | SRX21447928 | SRS18684551 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | wildtype plate 3 | GSM7728121 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | wildtype plate 3 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728121 | GSM7728121: wildtype plate 3; Danio rerio; RNA Seq | GSM7728121 r1 | GSM7728121 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | HUB-DB-006_HNWVVBGX9_S5_L002_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L002_R2_001.fastq.gz | fastq fastq | 987824896.0 | 11486336.0 | GSM7728121 r2 | 0:26 1:60 | A:251121714;C:184449811;G:201317783;T:350692225;N:243363 | 26 | 60 | 251121714 | 184449811 | 201317783 | 350692225 | 243363 | SRX21447928 | SRS18684551 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.11267 | 0.87874 | 0.10429 | 0.4457 | 0.99184 | 0.92498 | 0.56612 | 0.45489 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25249 | 25249 | SRR25723802 | SRX21447928 | SRS18684551 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | wildtype plate 3 | GSM7728121 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | wildtype plate 3 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728121 | GSM7728121: wildtype plate 3; Danio rerio; RNA Seq | GSM7728121 r1 | GSM7728121 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | HUB-DB-006_HNWVVBGX9_S5_L003_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L003_R2_001.fastq.gz | fastq fastq | 959933032.0 | 11162012.0 | GSM7728121 r3 | 0:26 1:60 | A:247983556;C:179564753;G:190342582;T:341858456;N:183685 | 26 | 60 | 247983556 | 179564753 | 190342582 | 341858456 | 183685 | SRX21447928 | SRS18684551 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.1118 | 0.87156 | 0.10348 | 0.43983 | 0.99149 | 0.93034 | 0.65287 | 0.44548 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25250 | 25250 | SRR25723803 | SRX21447928 | SRS18684551 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | wildtype plate 3 | GSM7728121 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | wildtype plate 3 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728121 | GSM7728121: wildtype plate 3; Danio rerio; RNA Seq | GSM7728121 r1 | GSM7728121 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | HUB-DB-006_HNWVVBGX9_S5_L004_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L004_R2_001.fastq.gz | fastq fastq | 798370766.0 | 9283381.0 | GSM7728121 r4 | 0:26 1:60 | A:205538880;C:148510556;G:161196381;T:282964175;N:160774 | 26 | 60 | 205538880 | 148510556 | 161196381 | 282964175 | 160774 | SRX21447928 | SRS18684551 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.11018 | 0.87017 | 0.10214 | 0.43625 | 0.99226 | 0.93332 | 0.56058 | 0.44211 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25251 | 25251 | SRR25723804 | SRX21447927 | SRS18684550 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | wildtype plate 2 | GSM7728120 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | wildtype plate 2 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728120 | GSM7728120: wildtype plate 2; Danio rerio; RNA Seq | GSM7728120 r1 | GSM7728120 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | 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 | GSM7728120 r1 | 0:26 1:60 | A:213590554;C:148614157;G:163804315;T:279996916;N:172592 | 26 | 60 | 213590554 | 148614157 | 163804315 | 279996916 | 172592 | SRX21447927 | SRS18684550 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.10778 | 0.79219 | 0.10092 | 0.39443 | 0.99255 | 0.93712 | 0.64412 | 0.39504 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25252 | 25252 | SRR25723805 | SRX21447927 | SRS18684550 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | wildtype plate 2 | GSM7728120 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | wildtype plate 2 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728120 | GSM7728120: wildtype plate 2; Danio rerio; RNA Seq | GSM7728120 r1 | GSM7728120 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | 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 | GSM7728120 r2 | 0:26 1:60 | A:227213153;C:160851586;G:182364146;T:303951184;N:214217 | 26 | 60 | 227213153 | 160851586 | 182364146 | 303951184 | 214217 | SRX21447927 | SRS18684550 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.11064 | 0.80317 | 0.1038 | 0.40093 | 0.99249 | 0.9332 | 0.652 | 0.40914 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25253 | 25253 | SRR25723806 | SRX21447927 | SRS18684550 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | wildtype plate 2 | GSM7728120 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | wildtype plate 2 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728120 | GSM7728120: wildtype plate 2; Danio rerio; RNA Seq | GSM7728120 r1 | GSM7728120 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | 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 | GSM7728120 r3 | 0:26 1:60 | A:220300204;C:153061412;G:168938657;T:289375449;N:160138 | 26 | 60 | 220300204 | 153061412 | 168938657 | 289375449 | 160138 | SRX21447927 | SRS18684550 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.10987 | 0.78665 | 0.10348 | 0.39264 | 0.99316 | 0.93661 | 0.66753 | 0.37676 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25254 | 25254 | SRR25723807 | SRX21447927 | SRS18684550 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | wildtype plate 2 | GSM7728120 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | wildtype plate 2 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728120 | GSM7728120: wildtype plate 2; Danio rerio; RNA Seq | GSM7728120 r1 | GSM7728120 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | HUB-DB-005_HNWVVBGX9_S4_L004_R2_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L004_R1_001.fastq.gz | fastq fastq | 692573136.0 | 8053176.0 | GSM7728120 r4 | 0:26 1:60 | A:182418113;C:126757471;G:143869511;T:239393143;N:134898 | 26 | 60 | 182418113 | 126757471 | 143869511 | 239393143 | 134898 | SRX21447927 | SRS18684550 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.10825 | 0.81365 | 0.10178 | 0.40513 | 0.99308 | 0.94032 | 0.67299 | 0.41125 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25255 | 25255 | SRR25723808 | SRX21447926 | SRS18684549 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | hmga1a mutant plate 2 | GSM7728119 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | hmga1a mutant plate 2 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728119 | GSM7728119: hmga1a mutant plate 2; Danio rerio; RNA Seq | GSM7728119 r1 | GSM7728119 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | HUB-DB-004_AHVKTGBGX7_S7_L001_R1_001.fastq.gz HUB-DB-004_AHVKTGBGX7_S7_L001_R2_001.fastq.gz | fastq fastq | 364147736.0 | 4234276.0 | GSM7728119 r1 | 0:26 1:60 | A:94538754;C:69024492;G:68361658;T:132108181;N:114651 | 26 | 60 | 94538754 | 69024492 | 68361658 | 132108181 | 114651 | SRX21447926 | SRS18684549 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.11558 | 0.78278 | 0.10659 | 0.24226 | 0.9893 | 0.92719 | 0.58692 | 0.48105 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25256 | 25256 | SRR25723809 | SRX21447926 | SRS18684549 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | hmga1a mutant plate 2 | GSM7728119 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | hmga1a mutant plate 2 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728119 | GSM7728119: hmga1a mutant plate 2; Danio rerio; RNA Seq | GSM7728119 r1 | GSM7728119 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | HUB-DB-004_AHVKTGBGX7_S7_L002_R1_001.fastq.gz HUB-DB-004_AHVKTGBGX7_S7_L002_R2_001.fastq.gz | fastq fastq | 377653262.0 | 4391317.0 | GSM7728119 r2 | 0:26 1:60 | A:99999342;C:71104204;G:70005970;T:136434888;N:108858 | 26 | 60 | 99999342 | 71104204 | 70005970 | 136434888 | 108858 | SRX21447926 | SRS18684549 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.11405 | 0.77996 | 0.10525 | 0.24008 | 0.98963 | 0.93616 | 0.60855 | 0.44129 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25257 | 25257 | SRR25723810 | SRX21447926 | SRS18684549 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | hmga1a mutant plate 2 | GSM7728119 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | hmga1a mutant plate 2 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728119 | GSM7728119: hmga1a mutant plate 2; Danio rerio; RNA Seq | GSM7728119 r1 | GSM7728119 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | HUB-DB-004_AHVKTGBGX7_S7_L003_R1_001.fastq.gz HUB-DB-004_AHVKTGBGX7_S7_L003_R2_001.fastq.gz | fastq fastq | 306947588.0 | 3569158.0 | GSM7728119 r3 | 0:26 1:60 | A:80261116;C:58220837;G:57196503;T:111195958;N:73174 | 26 | 60 | 80261116 | 58220837 | 57196503 | 111195958 | 73174 | SRX21447926 | SRS18684549 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.11141 | 0.76713 | 0.10254 | 0.23772 | 0.98938 | 0.93314 | 0.62261 | 0.47885 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25258 | 25258 | SRR25723811 | SRX21447926 | SRS18684549 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | hmga1a mutant plate 2 | GSM7728119 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | hmga1a mutant plate 2 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728119 | GSM7728119: hmga1a mutant plate 2; Danio rerio; RNA Seq | GSM7728119 r1 | GSM7728119 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | HUB-DB-004_AHVKTGBGX7_S7_L004_R1_001.fastq.gz HUB-DB-004_AHVKTGBGX7_S7_L004_R2_001.fastq.gz | fastq fastq | 389472414.0 | 4528749.0 | GSM7728119 r4 | 0:26 1:60 | A:102486709;C:73105388;G:73019179;T:140769931;N:91207 | 26 | 60 | 102486709 | 73105388 | 73019179 | 140769931 | 91207 | SRX21447926 | SRS18684549 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.11502 | 0.78307 | 0.10673 | 0.24219 | 0.98967 | 0.93308 | 0.64527 | 0.43659 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25259 | 25259 | SRR25723812 | SRX21447925 | SRS18684547 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | hmga1a mutant plate 1 | GSM7728118 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | hmga1a mutant plate 1 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728118 | GSM7728118: hmga1a mutant plate 1; Danio rerio; RNA Seq | GSM7728118 r1 | GSM7728118 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | HUB-DB-003_AHVKTGBGX7_S6_L001_R1_001.fastq.gz HUB-DB-003_AHVKTGBGX7_S6_L001_R2_001.fastq.gz | fastq fastq | 381365624.0 | 4434484.0 | GSM7728118 r1 | 0:26 1:60 | A:102130758;C:71032768;G:73641442;T:134437630;N:123026 | 26 | 60 | 102130758 | 71032768 | 73641442 | 134437630 | 123026 | SRX21447925 | SRS18684547 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.10052 | 0.7243 | 0.09214 | 0.25633 | 0.9892 | 0.92985 | 0.52345 | 0.5112 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25260 | 25260 | SRR25723813 | SRX21447925 | SRS18684547 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | hmga1a mutant plate 1 | GSM7728118 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | hmga1a mutant plate 1 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728118 | GSM7728118: hmga1a mutant plate 1; Danio rerio; RNA Seq | GSM7728118 r1 | GSM7728118 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | HUB-DB-003_AHVKTGBGX7_S6_L002_R1_001.fastq.gz HUB-DB-003_AHVKTGBGX7_S6_L002_R2_001.fastq.gz | fastq fastq | 400525220.0 | 4657270.0 | GSM7728118 r2 | 0:26 1:60 | A:109307778;C:73934198;G:76916762;T:140249156;N:117326 | 26 | 60 | 109307778 | 73934198 | 76916762 | 140249156 | 117326 | SRX21447925 | SRS18684547 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.09923 | 0.71601 | 0.09078 | 0.25139 | 0.98948 | 0.93914 | 0.52314 | 0.5078 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25261 | 25261 | SRR25723814 | SRX21447925 | SRS18684547 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | hmga1a mutant plate 1 | GSM7728118 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | hmga1a mutant plate 1 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728118 | GSM7728118: hmga1a mutant plate 1; Danio rerio; RNA Seq | GSM7728118 r1 | GSM7728118 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | HUB-DB-003_AHVKTGBGX7_S6_L003_R1_001.fastq.gz HUB-DB-003_AHVKTGBGX7_S6_L003_R2_001.fastq.gz | fastq fastq | 341364014.0 | 3969349.0 | GSM7728118 r3 | 0:26 1:60 | A:91716565;C:63676514;G:65563102;T:120323617;N:84216 | 26 | 60 | 91716565 | 63676514 | 65563102 | 120323617 | 84216 | SRX21447925 | SRS18684547 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.09826 | 0.7079 | 0.09008 | 0.2497 | 0.98918 | 0.93809 | 0.52649 | 0.49781 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25262 | 25262 | SRR25723815 | SRX21447925 | SRS18684547 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | hmga1a mutant plate 1 | GSM7728118 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | hmga1a mutant plate 1 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728118 | GSM7728118: hmga1a mutant plate 1; Danio rerio; RNA Seq | GSM7728118 r1 | GSM7728118 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | HUB-DB-003_AHVKTGBGX7_S6_L004_R1_001.fastq.gz HUB-DB-003_AHVKTGBGX7_S6_L004_R2_001.fastq.gz | fastq fastq | 414000732.0 | 4813962.0 | GSM7728118 r4 | 0:26 1:60 | A:112224009;C:76213738;G:80259829;T:145201785;N:101371 | 26 | 60 | 112224009 | 76213738 | 80259829 | 145201785 | 101371 | SRX21447925 | SRS18684547 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.10103 | 0.71981 | 0.09294 | 0.25413 | 0.98902 | 0.93669 | 0.52994 | 0.51172 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25263 | 25263 | SRR25723816 | SRX21447924 | SRS18684548 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | wildtype plate 1 | GSM7728117 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | wildtype plate 1 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728117 | GSM7728117: wildtype plate 1; Danio rerio; RNA Seq | GSM7728117 r1 | GSM7728117 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | 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 | GSM7728117 r1 | 0:26 1:60 | A:125045012;C:89627491;G:85413855;T:171466861;N:149815 | 26 | 60 | 125045012 | 89627491 | 85413855 | 171466861 | 149815 | SRX21447924 | SRS18684548 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.10906 | 0.68002 | 0.10212 | 0.30506 | 0.99101 | 0.94219 | 0.63738 | 0.45862 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25264 | 25264 | SRR25723817 | SRX21447924 | SRS18684548 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | wildtype plate 1 | GSM7728117 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | wildtype plate 1 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728117 | GSM7728117: wildtype plate 1; Danio rerio; RNA Seq | GSM7728117 r1 | GSM7728117 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | 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 | GSM7728117 r2 | 0:26 1:60 | A:131516821;C:92202683;G:88685608;T:176824985;N:142841 | 26 | 60 | 131516821 | 92202683 | 88685608 | 176824985 | 142841 | SRX21447924 | SRS18684548 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.11042 | 0.68086 | 0.10299 | 0.30411 | 0.99093 | 0.94856 | 0.60224 | 0.46578 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25265 | 25265 | SRR25723818 | SRX21447924 | SRS18684548 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | wildtype plate 1 | GSM7728117 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | wildtype plate 1 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728117 | GSM7728117: wildtype plate 1; Danio rerio; RNA Seq | GSM7728117 r1 | GSM7728117 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | 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 | GSM7728117 r3 | 0:26 1:60 | A:108841476;C:77418215;G:73171345;T:148203998;N:100254 | 26 | 60 | 108841476 | 77418215 | 73171345 | 148203998 | 100254 | SRX21447924 | SRS18684548 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.10882 | 0.67068 | 0.10177 | 0.29557 | 0.99151 | 0.94686 | 0.65762 | 0.42658 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 25266 | 25266 | SRR25723819 | SRX21447924 | SRS18684548 | SRP456323 | PRJNA1008049 | Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq] | GSE241390 | Transcriptome Analysis | The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3 7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin. | parent bioproject:PRJNA1006653 | pubmed:39747457 | wildtype plate 1 | GSM7728117 | source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing | wildtype plate 1 | Based on the distribution of the log10 total reads plotted against the frequency we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a / cells. Next single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes dimensions = 8 resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their genes and GO terms per module Supplementary files format and content: count tables transcriptcounts | adult heart | cryoinjury was performed 7 days before hearts were extracted | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury | GSM7728117 | GSM7728117: wildtype plate 1; Danio rerio; RNA Seq | GSM7728117 r1 | GSM7728117 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al. 2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP456323 | 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 | GSM7728117 r4 | 0:26 1:60 | A:135189083;C:94908231;G:92431583;T:182885125;N:125282 | 26 | 60 | 135189083 | 94908231 | 92431583 | 182885125 | 125282 | SRX21447924 | SRS18684548 | SRA1698978 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.10989 | 0.68603 | 0.10286 | 0.30542 | 0.99107 | 0.94777 | 0.65338 | 0.42121 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-08-22 | Adult | Adult | Heart | Cardiovascular System | ||||||||||
| 40164 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;