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131 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "celseq" and tissue_curation_coarse = "Cardiovascular System"

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devstage_curation 6

devstage_curation_coarse 5

tissue_curation 3

experiment.library_layout 2

tissue_curation_coarse 1

  • Cardiovascular System · 131 ✖

technology 1

  • celseq · 131 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 131 ✖

experiment.library_selection 1

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
38364 38364 SRR1793802 SRX869237 SRS840014 SRP053359 PRJNA274951 Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein GSE65751 Transcriptome Analysis How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment the nature of which is far from being clear. In the case of the lymphatic system venous endothelial cells are thought to give rise to lymphatic vessels through a process of trans differentiation. Upon expression of a set of transcription factors venous cells acquire a lymphatic fate and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish in combination with endothelial photoconvertible reporters and long term live imaging we demonstrate that these multipotent angioblasts can generate not only lymphatic but also arterious and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf 6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.   pubmed:25992545   d red ZF sample 0012 GSM1604058   tissue:Dorsal endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf d red ZF sample 0012 Libraries were sequenced on the Illumina HiSeq2500 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et al. 2012 demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules. Dorsal endothelial cells   RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 The vPCV vs dPCV endothelial cells were analyzed at 24hpf strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf GSM1604058 GSM1604058: d red ZF sample 0012; Danio rerio; RNA Seq GSM1604058   1 RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 GEO Accession:GSM1604058 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP053359     d_red_ZF_sample_0012.fastq.gz fastq 136949295.0 3912837.0 GSM1604058 r1 0:35 A:38967686;C:29235653;G:29781723;T:38764742;N:199491 35       38967686 29235653 29781723 38764742 199491 SRX869237 SRS840014 SRA236924 GEO Itai Yanai, Biology, Technion - Israel Institute of Technology 1 0.50546   0.22201   0.91524   0.49457   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2015-02-09 Pharyngula Embryo Endothelium Cardiovascular System
38365 38365 SRR1793801 SRX869236 SRS840015 SRP053359 PRJNA274951 Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein GSE65751 Transcriptome Analysis How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment the nature of which is far from being clear. In the case of the lymphatic system venous endothelial cells are thought to give rise to lymphatic vessels through a process of trans differentiation. Upon expression of a set of transcription factors venous cells acquire a lymphatic fate and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish in combination with endothelial photoconvertible reporters and long term live imaging we demonstrate that these multipotent angioblasts can generate not only lymphatic but also arterious and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf 6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.   pubmed:25992545   d red ZF sample 0008 GSM1604057   tissue:Dorsal endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf d red ZF sample 0008 Libraries were sequenced on the Illumina HiSeq2500 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et al. 2012 demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules. Dorsal endothelial cells   RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 The vPCV vs dPCV endothelial cells were analyzed at 24hpf strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf GSM1604057 GSM1604057: d red ZF sample 0008; Danio rerio; RNA Seq GSM1604057   1 RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 GEO Accession:GSM1604057 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP053359     d_red_ZF_sample_0008.fastq.gz fastq 230204380.0 6577268.0 GSM1604057 r1 0:35 A:63286154;C:49924891;G:50948035;T:65703538;N:341762 35       63286154 49924891 50948035 65703538 341762 SRX869236 SRS840015 SRA236924 GEO Itai Yanai, Biology, Technion - Israel Institute of Technology 1 0.59898   0.14092   0.89073   0.49292   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2015-02-09 Pharyngula Embryo Endothelium Cardiovascular System
38366 38366 SRR1793800 SRX869235 SRS840013 SRP053359 PRJNA274951 Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein GSE65751 Transcriptome Analysis How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment the nature of which is far from being clear. In the case of the lymphatic system venous endothelial cells are thought to give rise to lymphatic vessels through a process of trans differentiation. Upon expression of a set of transcription factors venous cells acquire a lymphatic fate and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish in combination with endothelial photoconvertible reporters and long term live imaging we demonstrate that these multipotent angioblasts can generate not only lymphatic but also arterious and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf 6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.   pubmed:25992545   V red ZF sample 0011 GSM1604056   tissue:Ventral endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf V red ZF sample 0011 Libraries were sequenced on the Illumina HiSeq2500 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et al. 2012 demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules. Ventral endothelial cells   RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 The vPCV vs dPCV endothelial cells were analyzed at 24hpf strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf GSM1604056 GSM1604056: V red ZF sample 0011; Danio rerio; RNA Seq GSM1604056   1 RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 GEO Accession:GSM1604056 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP053359     V_red_ZF_sample_0011.fastq.gz fastq 146319705.0 4180563.0 GSM1604056 r1 0:35 A:40991954;C:30892087;G:32112709;T:42103782;N:219173 35       40991954 30892087 32112709 42103782 219173 SRX869235 SRS840013 SRA236924 GEO Itai Yanai, Biology, Technion - Israel Institute of Technology 1 0.57038   0.16086   0.89014   0.53016   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2015-02-09 Pharyngula Embryo Endothelium Cardiovascular System
38367 38367 SRR1793799 SRX869234 SRS840016 SRP053359 PRJNA274951 Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein GSE65751 Transcriptome Analysis How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment the nature of which is far from being clear. In the case of the lymphatic system venous endothelial cells are thought to give rise to lymphatic vessels through a process of trans differentiation. Upon expression of a set of transcription factors venous cells acquire a lymphatic fate and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish in combination with endothelial photoconvertible reporters and long term live imaging we demonstrate that these multipotent angioblasts can generate not only lymphatic but also arterious and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf 6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.   pubmed:25992545   V red ZF sample 0007 GSM1604055   tissue:Ventral endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf V red ZF sample 0007 Libraries were sequenced on the Illumina HiSeq2500 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et al. 2012 demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules. Ventral endothelial cells   RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 The vPCV vs dPCV endothelial cells were analyzed at 24hpf strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf GSM1604055 GSM1604055: V red ZF sample 0007; Danio rerio; RNA Seq GSM1604055   1 RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 GEO Accession:GSM1604055 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP053359     V_red_ZF_sample_0007.fastq.gz fastq 219537045.0 6272487.0 GSM1604055 r1 0:35 A:61562432;C:46586451;G:48274564;T:62792331;N:321267 35       61562432 46586451 48274564 62792331 321267 SRX869234 SRS840016 SRA236924 GEO Itai Yanai, Biology, Technion - Israel Institute of Technology 1 0.57949   0.1659   0.88187   0.51446   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2015-02-09 Pharyngula Embryo Endothelium 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
47897 47897 SRR6908713 SRX3856801 SRS3100393 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM6 lymphocytes GSM3070139   tissue:WKM6 lymphocytes|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM6 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM6 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070139 GSM3070139: WKM6 lymphocytes; Danio rerio; RNA Seq GSM3070139   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070139 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM6_lymphocytes_L001_R1_001.fastq.gz WKM6_lymphocytes_L001_R2_001.fastq.gz fastq fastq 1092718271.0 7238113.0 GSM3070139 r1 0:75.49 1:75.48 A:308417237;C:162459915;G:183666585;T:438104581;N:69953 75 75     308417237 162459915 183666585 438104581 69953 SRX3856801 SRS3100393 SRA675960 GEO Hubrecht Institute 2 0.33032 0.81969 0.25647 0.49446 0.98587 0.93105 0.47765 0.53939 75 76 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47898 47898 SRR6908714 SRX3856801 SRS3100393 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM6 lymphocytes GSM3070139   tissue:WKM6 lymphocytes|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM6 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM6 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070139 GSM3070139: WKM6 lymphocytes; Danio rerio; RNA Seq GSM3070139   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070139 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM6_lymphocytes_L002_R1_001.fastq.gz WKM6_lymphocytes_L002_R2_001.fastq.gz fastq fastq 988686695.0 6550079.0 GSM3070139 r2 0:75.49 1:75.46 A:281384679;C:146335731;G:165878017;T:395040397;N:47871 75 75     281384679 146335731 165878017 395040397 47871 SRX3856801 SRS3100393 SRA675960 GEO Hubrecht Institute 2 0.31311 0.79325 0.23663 0.48843 0.99034 0.95471 0.47178 0.54622 75 76 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47899 47899 SRR6908715 SRX3856801 SRS3100393 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM6 lymphocytes GSM3070139   tissue:WKM6 lymphocytes|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM6 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM6 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070139 GSM3070139: WKM6 lymphocytes; Danio rerio; RNA Seq GSM3070139   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070139 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM6_lymphocytes_L003_R1_001.fastq.gz WKM6_lymphocytes_L003_R2_001.fastq.gz fastq fastq 965970467.0 6397966.0 GSM3070139 r3 0:75.51 1:75.47 A:271037832;C:143188198;G:162584210;T:389145889;N:14338 75 75     271037832 143188198 162584210 389145889 14338 SRX3856801 SRS3100393 SRA675960 GEO Hubrecht Institute 2 0.2983 0.81397 0.23255 0.49479 0.99377 0.94379 0.43187 0.54702 76 76 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47900 47900 SRR6908716 SRX3856801 SRS3100393 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM6 lymphocytes GSM3070139   tissue:WKM6 lymphocytes|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM6 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM6 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070139 GSM3070139: WKM6 lymphocytes; Danio rerio; RNA Seq GSM3070139   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070139 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM6_lymphocytes_L004_R1_001.fastq.gz WKM6_lymphocytes_L004_R2_001.fastq.gz fastq fastq 845107841.0 5598430.0 GSM3070139 r4 0:75.50 1:75.46 A:239787549;C:124312776;G:144002735;T:336997076;N:7705 75 75     239787549 124312776 144002735 336997076 7705 SRX3856801 SRS3100393 SRA675960 GEO Hubrecht Institute 2 0.27606 0.8077 0.21352 0.49895 0.99502 0.95511 0.37654 0.5537 76 76 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47905 47905 SRR6908705 SRX3856799 SRS3100391 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM5 lymphocytes GSM3070137   tissue:WKM5 lymphocytes|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM5 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM5 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070137 GSM3070137: WKM5 lymphocytes; Danio rerio; RNA Seq GSM3070137   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070137 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM5_lymphocytes_L001_R1_001.fastq.gz WKM5_lymphocytes_L001_R2_001.fastq.gz fastq fastq 989705998.0 6559370.0 GSM3070137 r1 0:75.45 1:75.43 A:297302138;C:149495824;G:174348330;T:368343979;N:215727 75 75     297302138 149495824 174348330 368343979 215727 SRX3856799 SRS3100391 SRA675960 GEO Hubrecht Institute 2 0.24742 0.6658 0.20828 0.41062 0.98214 0.85423 0.46204 0.47999 76 76 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47906 47906 SRR6908706 SRX3856799 SRS3100391 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM5 lymphocytes GSM3070137   tissue:WKM5 lymphocytes|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM5 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM5 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070137 GSM3070137: WKM5 lymphocytes; Danio rerio; RNA Seq GSM3070137   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070137 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM5_lymphocytes_L002_R1_001.fastq.gz WKM5_lymphocytes_L002_R2_001.fastq.gz fastq fastq 966752947.0 6406981.0 GSM3070137 r2 0:75.44 1:75.45 A:289601664;C:144620642;G:173993992;T:358339663;N:196986 75 75     289601664 144620642 173993992 358339663 196986 SRX3856799 SRS3100391 SRA675960 GEO Hubrecht Institute 2 0.23604 0.65405 0.20033 0.39718 0.98196 0.8636 0.50139 0.50729 74 76 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47907 47907 SRR6908707 SRX3856799 SRS3100391 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM5 lymphocytes GSM3070137   tissue:WKM5 lymphocytes|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM5 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM5 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070137 GSM3070137: WKM5 lymphocytes; Danio rerio; RNA Seq GSM3070137   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070137 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM5_lymphocytes_L003_R1_001.fastq.gz WKM5_lymphocytes_L003_R2_001.fastq.gz fastq fastq 958861430.0 6354224.0 GSM3070137 r3 0:75.46 1:75.44 A:286188763;C:145686623;G:169054587;T:357878024;N:53433 75 75     286188763 145686623 169054587 357878024 53433 SRX3856799 SRS3100391 SRA675960 GEO Hubrecht Institute 2 0.25215 0.67286 0.20951 0.41571 0.98707 0.84611 0.45707 0.51523 75 75 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47908 47908 SRR6908708 SRX3856799 SRS3100391 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM5 lymphocytes GSM3070137   tissue:WKM5 lymphocytes|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM5 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM5 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070137 GSM3070137: WKM5 lymphocytes; Danio rerio; RNA Seq GSM3070137   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070137 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM5_lymphocytes_L004_R2_001.fastq.gz WKM5_lymphocytes_L004_R1_001.fastq.gz fastq fastq 907053718.0 6010618.0 GSM3070137 r4 0:75.45 1:75.46 A:270238988;C:137187310;G:162483694;T:337104230;N:39496 75 75     270238988 137187310 162483694 337104230 39496 SRX3856799 SRS3100391 SRA675960 GEO Hubrecht Institute 2 0.2382 0.66089 0.20055 0.40225 0.98537 0.86109 0.4862 0.51182 75 74 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47953 47953 SRR6908655 SRX3856786 SRS3100377 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM10 lymphocytes GSM3070125   tissue:WKM10 lymphocytes|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM10 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM10 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070125 GSM3070125: WKM10 lymphocytes; Danio rerio; RNA Seq GSM3070125   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070125 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM10_lymphocytes_L001_R1_001.fastq.gz WKM10_lymphocytes_L001_R2_001.fastq.gz fastq fastq 1505229869.0 9975689.0 GSM3070125 r1 0:75.46 1:75.43 A:446863117;C:223332557;G:257023910;T:577686078;N:324207 75 75     446863117 223332557 257023910 577686078 324207 SRX3856786 SRS3100377 SRA675960 GEO Hubrecht Institute 2 0.27651 0.70172 0.22976 0.41642 0.98198 0.85401 0.46672 0.52056 75 76 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47954 47954 SRR6908656 SRX3856786 SRS3100377 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM10 lymphocytes GSM3070125   tissue:WKM10 lymphocytes|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM10 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM10 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070125 GSM3070125: WKM10 lymphocytes; Danio rerio; RNA Seq GSM3070125   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070125 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM10_lymphocytes_L002_R1_001.fastq.gz WKM10_lymphocytes_L002_R2_001.fastq.gz fastq fastq 1466970503.0 9721974.0 GSM3070125 r2 0:75.45 1:75.44 A:434939637;C:215624726;G:255310153;T:560791208;N:304779 75 75     434939637 215624726 255310153 560791208 304779 SRX3856786 SRS3100377 SRA675960 GEO Hubrecht Institute 2 0.263 0.6934 0.21939 0.4057 0.98127 0.86417 0.4805 0.49132 75 76 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47955 47955 SRR6908657 SRX3856786 SRS3100377 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM10 lymphocytes GSM3070125   tissue:WKM10 lymphocytes|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM10 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM10 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070125 GSM3070125: WKM10 lymphocytes; Danio rerio; RNA Seq GSM3070125   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070125 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM10_lymphocytes_L003_R2_001.fastq.gz WKM10_lymphocytes_L003_R1_001.fastq.gz fastq fastq 1456610152.0 9652493.0 GSM3070125 r3 0:75.46 1:75.44 A:429303329;C:217559734;G:249207876;T:560459433;N:79780 75 75     429303329 217559734 249207876 560459433 79780 SRX3856786 SRS3100377 SRA675960 GEO Hubrecht Institute 2 0.28238 0.70747 0.2323 0.4212 0.98683 0.84575 0.43386 0.5155 76 75 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47956 47956 SRR6908658 SRX3856786 SRS3100377 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM10 lymphocytes GSM3070125   tissue:WKM10 lymphocytes|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM10 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM10 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070125 GSM3070125: WKM10 lymphocytes; Danio rerio; RNA Seq GSM3070125   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070125 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM10_lymphocytes_L004_R1_001.fastq.gz WKM10_lymphocytes_L004_R2_001.fastq.gz fastq fastq 1372270103.0 9093444.0 GSM3070125 r4 0:75.46 1:75.45 A:404750065;C:203942354;G:237441524;T:526077075;N:59085 75 75     404750065 203942354 237441524 526077075 59085 SRX3856786 SRS3100377 SRA675960 GEO Hubrecht Institute 2 0.2714 0.69516 0.22843 0.40836 0.98602 0.8607 0.47846 0.52284 76 76 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System 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
55365 55365 SRR10321288 SRX7032108 SRS5552214 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   FK2 GSM4134187   source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle FK2 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgnppa:mCitrine ventricle 7dpi Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016   Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle GSM4134187 GSM4134187: FK2; Danio rerio; RNA Seq GSM4134187   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016 GEO Accession:GSM4134187 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     Fk-2_H3MHFBGXY_S4_L001_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L001_R2_001.fastq.gz fastq fastq 2747645940.0 18195462.0 GSM4134187 r1 0:75.51 1:75.50 A:761850296;C:390951746;G:422952266;T:1169751842;N:2139790 75 75     761850296 390951746 422952266 1169751842 2139790 SRX7032108 SRS5552214 SRA982819 GEO Bakkers, Hubrecht Institute 2 0.23534 0.89135 0.19366 0.15359 0.99902 0.86636 0.40119 0.71094 75 76 T B mate1 technical by mapping diff illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Multi-stage Multi-stage Heart Cardiovascular System
55366 55366 SRR10321289 SRX7032108 SRS5552214 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   FK2 GSM4134187   source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle FK2 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgnppa:mCitrine ventricle 7dpi Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016   Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle GSM4134187 GSM4134187: FK2; Danio rerio; RNA Seq GSM4134187   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016 GEO Accession:GSM4134187 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     Fk-2_H3MHFBGXY_S4_L002_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L002_R2_001.fastq.gz fastq fastq 2719577388.0 18010558.0 GSM4134187 r2 0:75.50 1:75.50 A:750500832;C:383761329;G:435629268;T:1147504474;N:2181485 75 75     750500832 383761329 435629268 1147504474 2181485 SRX7032108 SRS5552214 SRA982819 GEO Bakkers, Hubrecht Institute 2 0.21913 0.88799 0.16554 0.15559 0.99855 0.8704 0.48175 0.71083 76 76 T B mate1 technical by mapping diff illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Multi-stage Multi-stage Heart Cardiovascular System
55367 55367 SRR10321290 SRX7032108 SRS5552214 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   FK2 GSM4134187   source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle FK2 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgnppa:mCitrine ventricle 7dpi Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016   Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle GSM4134187 GSM4134187: FK2; Danio rerio; RNA Seq GSM4134187   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016 GEO Accession:GSM4134187 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     Fk-2_H3MHFBGXY_S4_L003_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L003_R2_001.fastq.gz fastq fastq 2396848795.0 15867573.0 GSM4134187 r3 0:75.56 1:75.50 A:649358056;C:340829352;G:366620430;T:1039511314;N:529643 75 75     649358056 340829352 366620430 1039511314 529643 SRX7032108 SRS5552214 SRA982819 GEO Bakkers, Hubrecht Institute 2 0.22581 0.89171 0.18682 0.15894 0.99928 0.87054 0.41592 0.70495 75 76 T B mate1 technical by mapping diff illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Multi-stage Multi-stage Heart Cardiovascular System
55368 55368 SRR10321291 SRX7032108 SRS5552214 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   FK2 GSM4134187   source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle FK2 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgnppa:mCitrine ventricle 7dpi Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016   Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle GSM4134187 GSM4134187: FK2; Danio rerio; RNA Seq GSM4134187   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016 GEO Accession:GSM4134187 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     Fk-2_H3MHFBGXY_S4_L004_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L004_R2_001.fastq.gz fastq fastq 2610671390.0 17282452.0 GSM4134187 r4 0:75.56 1:75.50 A:691899084;C:368646569;G:415634004;T:1133907995;N:583738 75 75     691899084 368646569 415634004 1133907995 583738 SRX7032108 SRS5552214 SRA982819 GEO Bakkers, Hubrecht Institute 2 0.24107 0.8886 0.19934 0.15491 0.99926 0.8702 0.31578 0.66998 76 76 T B mate1 technical by mapping diff illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Multi-stage Multi-stage Heart Cardiovascular System
55369 55369 SRR10321284 SRX7032107 SRS5552213 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   FK1 GSM4134186   source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle FK1 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgnppa:mCitrine ventricle 7dpi Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016   Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle GSM4134186 GSM4134186: FK1; Danio rerio; RNA Seq GSM4134186   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016 GEO Accession:GSM4134186 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     FK-1_H3MHFBGXY_S3_L001_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L001_R2_001.fastq.gz fastq fastq 2366670719.0 15672127.0 GSM4134186 r1 0:75.50 1:75.51 A:648000254;C:343663478;G:358343004;T:1014831853;N:1832130 75 75     648000254 343663478 358343004 1014831853 1832130 SRX7032107 SRS5552213 SRA982819 GEO Bakkers, Hubrecht Institute 2 0.30353 0.90485 0.25842 0.14878 0.99912 0.85857 0.23863 0.71645 76 75 T B mate1 technical by mapping diff illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Multi-stage Multi-stage Heart Cardiovascular System
55370 55370 SRR10321285 SRX7032107 SRS5552213 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   FK1 GSM4134186   source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle FK1 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgnppa:mCitrine ventricle 7dpi Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016   Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle GSM4134186 GSM4134186: FK1; Danio rerio; RNA Seq GSM4134186   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016 GEO Accession:GSM4134186 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     FK-1_H3MHFBGXY_S3_L002_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L002_R2_001.fastq.gz fastq fastq 2360571906.0 15632617.0 GSM4134186 r2 0:75.49 1:75.51 A:643644738;C:339965378;G:371359828;T:1003716606;N:1885356 75 75     643644738 339965378 371359828 1003716606 1885356 SRX7032107 SRS5552213 SRA982819 GEO Bakkers, Hubrecht Institute                       T B mate1 technical by mapping diff illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Multi-stage Multi-stage Heart Cardiovascular System
55371 55371 SRR10321286 SRX7032107 SRS5552213 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   FK1 GSM4134186   source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle FK1 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgnppa:mCitrine ventricle 7dpi Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016   Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle GSM4134186 GSM4134186: FK1; Danio rerio; RNA Seq GSM4134186   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016 GEO Accession:GSM4134186 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     FK-1_H3MHFBGXY_S3_L003_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L003_R2_001.fastq.gz fastq fastq 2074411223.0 13732357.0 GSM4134186 r3 0:75.55 1:75.51 A:554276583;C:300804770;G:312025485;T:906833457;N:470928 75 75     554276583 300804770 312025485 906833457 470928 SRX7032107 SRS5552213 SRA982819 GEO Bakkers, Hubrecht Institute 2 0.2996 0.90397 0.25521 0.15245 0.99933 0.86314 0.21969 0.69653 75 76 T B mate1 technical by mapping diff illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Multi-stage Multi-stage Heart Cardiovascular System
55372 55372 SRR10321287 SRX7032107 SRS5552213 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   FK1 GSM4134186   source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle FK1 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgnppa:mCitrine ventricle 7dpi Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016   Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle GSM4134186 GSM4134186: FK1; Danio rerio; RNA Seq GSM4134186   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016 GEO Accession:GSM4134186 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     FK-1_H3MHFBGXY_S3_L004_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L004_R2_001.fastq.gz fastq fastq 2267459781.0 15009993.0 GSM4134186 r4 0:75.55 1:75.51 A:592957170;C:326713096;G:354670327;T:992614149;N:505039 75 75     592957170 326713096 354670327 992614149 505039 SRX7032107 SRS5552213 SRA982819 GEO Bakkers, Hubrecht Institute 2 0.3137 0.9006 0.26295 0.14953 0.99914 0.8622 0.19895 0.70141 76 76 T B mate1 technical by mapping diff illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Multi-stage Multi-stage Heart Cardiovascular System
59985 59985 SRR12083057 SRX8610203 SRS6899881 SRP268691 PRJNA641676 Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration GSE153170 Transcriptome Analysis Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms such as zebrafish cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b / n=20 ventricles. All cells were sent for single cell RNA sequencing.   pubmed:34486669   HUB DB 012 GSM4635178   tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle HUB DB 012 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following order: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values Epicardial cells of the Zebrafish heart ventricle Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016.   line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle GSM4635178 GSM4635178: HUB DB 012; Danio rerio; RNA Seq GSM4635178   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016. GEO Accession:GSM4635178 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP268691     HUB-DB-012_H3HCLBGXC_S4_L001_R1_001.fastq.gz HUB-DB-012_H3HCLBGXC_S4_L001_R2_001.fastq.gz fastq fastq 623629172.0 7251502.0 GSM4635178 r1 0:26 1:60 A:152264664;C:116216632;G:110007461;T:245137012;N:3403 26 60     152264664 116216632 110007461 245137012 3403 SRX8610203 SRS6899881 SRA1090808 GEO Hubrecht 2 0.10748 0.88943 0.10172 0.27473 0.9931 0.82905 0.60372 0.48618 26 60 T B sc-like readlen illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2020-06-24 Adult Adult Heart Cardiovascular System
59986 59986 SRR12083058 SRX8610203 SRS6899881 SRP268691 PRJNA641676 Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration GSE153170 Transcriptome Analysis Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms such as zebrafish cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b / n=20 ventricles. All cells were sent for single cell RNA sequencing.   pubmed:34486669   HUB DB 012 GSM4635178   tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle HUB DB 012 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following order: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values Epicardial cells of the Zebrafish heart ventricle Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016.   line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle GSM4635178 GSM4635178: HUB DB 012; Danio rerio; RNA Seq GSM4635178   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016. GEO Accession:GSM4635178 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP268691     HUB-DB-012_H3HCLBGXC_S4_L002_R1_001.fastq.gz HUB-DB-012_H3HCLBGXC_S4_L002_R2_001.fastq.gz fastq fastq 597918268.0 6952538.0 GSM4635178 r2 0:26 1:60 A:145156634;C:110841797;G:108031654;T:233885695;N:2488 26 60     145156634 110841797 108031654 233885695 2488 SRX8610203 SRS6899881 SRA1090808 GEO Hubrecht 2 0.10741 0.88528 0.10165 0.27242 0.99289 0.82994 0.60407 0.47918 26 60 T B sc-like readlen illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2020-06-24 Adult Adult Heart Cardiovascular System
59987 59987 SRR12083059 SRX8610203 SRS6899881 SRP268691 PRJNA641676 Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration GSE153170 Transcriptome Analysis Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms such as zebrafish cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b / n=20 ventricles. All cells were sent for single cell RNA sequencing.   pubmed:34486669   HUB DB 012 GSM4635178   tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle HUB DB 012 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following order: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values Epicardial cells of the Zebrafish heart ventricle Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016.   line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle GSM4635178 GSM4635178: HUB DB 012; Danio rerio; RNA Seq GSM4635178   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016. GEO Accession:GSM4635178 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP268691     HUB-DB-012_H3HCLBGXC_S4_L003_R1_001.fastq.gz HUB-DB-012_H3HCLBGXC_S4_L003_R2_001.fastq.gz fastq fastq 628530140.0 7308490.0 GSM4635178 r3 0:26 1:60 A:153358630;C:117237955;G:110777080;T:247131309;N:25166 26 60     153358630 117237955 110777080 247131309 25166 SRX8610203 SRS6899881 SRA1090808 GEO Hubrecht 2 0.10839 0.88927 0.10281 0.27315 0.99316 0.8284 0.62118 0.46755 26 60 T B sc-like readlen illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2020-06-24 Adult Adult Heart Cardiovascular System
59988 59988 SRR12083060 SRX8610203 SRS6899881 SRP268691 PRJNA641676 Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration GSE153170 Transcriptome Analysis Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms such as zebrafish cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b / n=20 ventricles. All cells were sent for single cell RNA sequencing.   pubmed:34486669   HUB DB 012 GSM4635178   tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle HUB DB 012 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following order: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values Epicardial cells of the Zebrafish heart ventricle Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016.   line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle GSM4635178 GSM4635178: HUB DB 012; Danio rerio; RNA Seq GSM4635178   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016. GEO Accession:GSM4635178 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP268691     HUB-DB-012_H3HCLBGXC_S4_L004_R1_001.fastq.gz HUB-DB-012_H3HCLBGXC_S4_L004_R2_001.fastq.gz fastq fastq 605801372.0 7044202.0 GSM4635178 r4 0:26 1:60 A:147072053;C:112438811;G:109075558;T:237165161;N:49789 26 60     147072053 112438811 109075558 237165161 49789 SRX8610203 SRS6899881 SRA1090808 GEO Hubrecht 2 0.10729 0.88592 0.10142 0.2715 0.99318 0.83096 0.63628 0.47975 26 60 T B sc-like readlen illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2020-06-24 Adult Adult Heart Cardiovascular System
59989 59989 SRR12083053 SRX8610202 SRS6899880 SRP268691 PRJNA641676 Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration GSE153170 Transcriptome Analysis Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms such as zebrafish cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b / n=20 ventricles. All cells were sent for single cell RNA sequencing.   pubmed:34486669   HUB DB 011 GSM4635177   tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle HUB DB 011 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following order: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values Epicardial cells of the Zebrafish heart ventricle Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016.   line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle GSM4635177 GSM4635177: HUB DB 011; Danio rerio; RNA Seq GSM4635177   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016. GEO Accession:GSM4635177 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP268691     HUB-DB-011_H3HCLBGXC_S3_L001_R1_001.fastq.gz HUB-DB-011_H3HCLBGXC_S3_L001_R2_001.fastq.gz fastq fastq 634797476.0 7381366.0 GSM4635177 r1 0:26 1:60 A:153195131;C:118480864;G:115080449;T:248037462;N:3570 26 60     153195131 118480864 115080449 248037462 3570 SRX8610202 SRS6899880 SRA1090808 GEO Hubrecht 2 0.11082 0.89281 0.10414 0.28784 0.99204 0.82619 0.66824 0.50609 26 60 T B sc-like readlen illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2020-06-24 Adult Adult Heart Cardiovascular System
59990 59990 SRR12083054 SRX8610202 SRS6899880 SRP268691 PRJNA641676 Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration GSE153170 Transcriptome Analysis Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms such as zebrafish cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b / n=20 ventricles. All cells were sent for single cell RNA sequencing.   pubmed:34486669   HUB DB 011 GSM4635177   tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle HUB DB 011 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following order: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values Epicardial cells of the Zebrafish heart ventricle Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016.   line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle GSM4635177 GSM4635177: HUB DB 011; Danio rerio; RNA Seq GSM4635177   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016. GEO Accession:GSM4635177 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP268691     HUB-DB-011_H3HCLBGXC_S3_L002_R1_001.fastq.gz HUB-DB-011_H3HCLBGXC_S3_L002_R2_001.fastq.gz fastq fastq 611046770.0 7105195.0 GSM4635177 r2 0:26 1:60 A:146818280;C:113612783;G:112799955;T:237813147;N:2605 26 60     146818280 113612783 112799955 237813147 2605 SRX8610202 SRS6899880 SRA1090808 GEO Hubrecht 2 0.11194 0.89124 0.10494 0.28808 0.99275 0.83071 0.67141 0.50375 26 60 T B sc-like readlen illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2020-06-24 Adult Adult Heart Cardiovascular System
59991 59991 SRR12083055 SRX8610202 SRS6899880 SRP268691 PRJNA641676 Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration GSE153170 Transcriptome Analysis Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms such as zebrafish cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b / n=20 ventricles. All cells were sent for single cell RNA sequencing.   pubmed:34486669   HUB DB 011 GSM4635177   tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle HUB DB 011 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following order: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values Epicardial cells of the Zebrafish heart ventricle Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016.   line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle GSM4635177 GSM4635177: HUB DB 011; Danio rerio; RNA Seq GSM4635177   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016. GEO Accession:GSM4635177 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP268691     HUB-DB-011_H3HCLBGXC_S3_L003_R1_001.fastq.gz HUB-DB-011_H3HCLBGXC_S3_L003_R2_001.fastq.gz fastq fastq 641591132.0 7460362.0 GSM4635177 r3 0:26 1:60 A:154776835;C:119807925;G:116219737;T:250759686;N:26949 26 60     154776835 119807925 116219737 250759686 26949 SRX8610202 SRS6899880 SRA1090808 GEO Hubrecht 2 0.11171 0.8947 0.10479 0.29095 0.99233 0.82775 0.69148 0.50141 26 60 T B sc-like readlen illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2020-06-24 Adult Adult Heart Cardiovascular System
59992 59992 SRR12083056 SRX8610202 SRS6899880 SRP268691 PRJNA641676 Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration GSE153170 Transcriptome Analysis Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms such as zebrafish cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b / n=20 ventricles. All cells were sent for single cell RNA sequencing.   pubmed:34486669   HUB DB 011 GSM4635177   tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle HUB DB 011 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following order: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values Epicardial cells of the Zebrafish heart ventricle Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016.   line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle GSM4635177 GSM4635177: HUB DB 011; Danio rerio; RNA Seq GSM4635177   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016. GEO Accession:GSM4635177 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP268691     HUB-DB-011_H3HCLBGXC_S3_L004_R1_001.fastq.gz HUB-DB-011_H3HCLBGXC_S3_L004_R2_001.fastq.gz fastq fastq 619988534.0 7209169.0 GSM4635177 r4 0:26 1:60 A:149057849;C:115334020;G:114131475;T:241414817;N:50373 26 60     149057849 115334020 114131475 241414817 50373 SRX8610202 SRS6899880 SRA1090808 GEO Hubrecht 2 0.11255 0.89073 0.10573 0.28703 0.99283 0.83061 0.6874 0.50364 26 60 T B sc-like readlen illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2020-06-24 Adult Adult Heart Cardiovascular System
59993 59993 SRR12083049 SRX8610201 SRS6899879 SRP268691 PRJNA641676 Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration GSE153170 Transcriptome Analysis Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms such as zebrafish cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b / n=20 ventricles. All cells were sent for single cell RNA sequencing.   pubmed:34486669   HUB DB 010 GSM4635176   tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle HUB DB 010 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following order: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values Epicardial cells of the Zebrafish heart ventricle Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016.   line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle GSM4635176 GSM4635176: HUB DB 010; Danio rerio; RNA Seq GSM4635176   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016. GEO Accession:GSM4635176 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP268691     HUB-DB-010_H3HCLBGXC_S2_L001_R1_001.fastq.gz HUB-DB-010_H3HCLBGXC_S2_L001_R2_001.fastq.gz fastq fastq 673568770.0 7832195.0 GSM4635176 r1 0:26 1:60 A:164220958;C:127417067;G:127429427;T:254497649;N:3669 26 60     164220958 127417067 127429427 254497649 3669 SRX8610201 SRS6899879 SRA1090808 GEO Hubrecht 2 0.10904 0.86908 0.10146 0.28252 0.99086 0.83952 0.55689 0.51097 26 60 T B sc-like readlen illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2020-06-24 Adult Adult Heart Cardiovascular System
59994 59994 SRR12083050 SRX8610201 SRS6899879 SRP268691 PRJNA641676 Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration GSE153170 Transcriptome Analysis Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms such as zebrafish cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b / n=20 ventricles. All cells were sent for single cell RNA sequencing.   pubmed:34486669   HUB DB 010 GSM4635176   tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle HUB DB 010 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following order: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values Epicardial cells of the Zebrafish heart ventricle Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016.   line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle GSM4635176 GSM4635176: HUB DB 010; Danio rerio; RNA Seq GSM4635176   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016. GEO Accession:GSM4635176 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP268691     HUB-DB-010_H3HCLBGXC_S2_L002_R1_001.fastq.gz HUB-DB-010_H3HCLBGXC_S2_L002_R2_001.fastq.gz fastq fastq 642282486.0 7468401.0 GSM4635176 r2 0:26 1:60 A:156140841;C:120979080;G:123582811;T:241577191;N:2563 26 60     156140841 120979080 123582811 241577191 2563 SRX8610201 SRS6899879 SRA1090808 GEO Hubrecht 2 0.10877 0.86702 0.10115 0.2848 0.98961 0.84122 0.5621 0.48392 26 60 T B sc-like readlen illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2020-06-24 Adult Adult Heart Cardiovascular System
59995 59995 SRR12083051 SRX8610201 SRS6899879 SRP268691 PRJNA641676 Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration GSE153170 Transcriptome Analysis Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms such as zebrafish cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b / n=20 ventricles. All cells were sent for single cell RNA sequencing.   pubmed:34486669   HUB DB 010 GSM4635176   tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle HUB DB 010 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following order: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values Epicardial cells of the Zebrafish heart ventricle Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016.   line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle GSM4635176 GSM4635176: HUB DB 010; Danio rerio; RNA Seq GSM4635176   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016. GEO Accession:GSM4635176 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP268691     HUB-DB-010_H3HCLBGXC_S2_L003_R1_001.fastq.gz HUB-DB-010_H3HCLBGXC_S2_L003_R2_001.fastq.gz fastq fastq 676661932.0 7868162.0 GSM4635176 r3 0:26 1:60 A:165121933;C:128034418;G:127770885;T:255708762;N:25934 26 60     165121933 128034418 127770885 255708762 25934 SRX8610201 SRS6899879 SRA1090808 GEO Hubrecht 2 0.10987 0.87058 0.103 0.282 0.99109 0.83915 0.55503 0.51595 26 60 T B sc-like readlen illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2020-06-24 Adult Adult Heart Cardiovascular System
59996 59996 SRR12083052 SRX8610201 SRS6899879 SRP268691 PRJNA641676 Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration GSE153170 Transcriptome Analysis Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms such as zebrafish cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b / n=20 ventricles. All cells were sent for single cell RNA sequencing.   pubmed:34486669   HUB DB 010 GSM4635176   tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle HUB DB 010 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following order: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values Epicardial cells of the Zebrafish heart ventricle Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016.   line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle GSM4635176 GSM4635176: HUB DB 010; Danio rerio; RNA Seq GSM4635176   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016. GEO Accession:GSM4635176 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP268691     HUB-DB-010_H3HCLBGXC_S2_L004_R1_001.fastq.gz HUB-DB-010_H3HCLBGXC_S2_L004_R2_001.fastq.gz fastq fastq 649298624.0 7549984.0 GSM4635176 r4 0:26 1:60 A:158062491;C:122309175;G:124562965;T:244314794;N:49199 26 60     158062491 122309175 124562965 244314794 49199 SRX8610201 SRS6899879 SRA1090808 GEO Hubrecht 2 0.11052 0.86686 0.1033 0.2819 0.99052 0.84066 0.55805 0.50641 26 60 T B sc-like readlen illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2020-06-24 Adult Adult Heart Cardiovascular System
59997 59997 SRR12083045 SRX8610200 SRS6899878 SRP268691 PRJNA641676 Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration GSE153170 Transcriptome Analysis Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms such as zebrafish cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b / n=20 ventricles. All cells were sent for single cell RNA sequencing.   pubmed:34486669   HUB DB 009 GSM4635175   tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle HUB DB 009 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following order: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values Epicardial cells of the Zebrafish heart ventricle Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates each well containing 1 cell. Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016.   line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle GSM4635175 GSM4635175: HUB DB 009; Danio rerio; RNA Seq GSM4635175   1 Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for library prep Hashimony et al. 2016. GEO Accession:GSM4635175 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP268691     HUB-DB-009_H3HCLBGXC_S1_L001_R1_001.fastq.gz HUB-DB-009_H3HCLBGXC_S1_L001_R2_001.fastq.gz fastq fastq 893990210.0 10395235.0 GSM4635175 r1 0:26 1:60 A:217651633;C:169265774;G:172112042;T:334955815;N:4946 26 60     217651633 169265774 172112042 334955815 4946 SRX8610200 SRS6899878 SRA1090808 GEO Hubrecht 2 0.1006 0.81888 0.09561 0.29404 0.99318 0.83806 0.67678 0.52964 26 60 T B sc-like readlen illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2020-06-24 Adult Adult Heart Cardiovascular System

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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");;