metadata: run_metadata: 62 rows where experiment.library_layout = "SINGLE", technology = "celseq" and tissue_curation

62 rows where experiment.library_layout = "SINGLE", technology = "celseq" and tissue_curation_coarse = "Cardiovascular System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
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
48190	48190	SRR7119875	SRX4041518	SRS3258997	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 3dpf mut 44	GSM3131266	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 3dpf mut 44	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	GSM3131266	GSM3131266: Danio rerio RNAseq singleHeart 3dpf mut 44; Danio rerio; RNA Seq	GSM3131266	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131266	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_44_NDCII_sample_0044.fastq.gz	fastq	182748450.0	2436646.0	GSM3131266 r1	0:75	A:58073626;C:30410206;G:39711272;T:54442336;N:111010	75	58073626	30410206	39711272	54442336	111010	SRX4041518	SRS3258997	SRA699717	GEO	Molecular Biology, Radboud University	1	0.60972	0.21593	0.85427	0.51332	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48191	48191	SRR7119874	SRX4041517	SRS3258996	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 3dpf mut 43	GSM3131265	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 3dpf mut 43	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	GSM3131265	GSM3131265: Danio rerio RNAseq singleHeart 3dpf mut 43; Danio rerio; RNA Seq	GSM3131265	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131265	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_43_NDCII_sample_0043.fastq.gz	fastq	91153575.0	1215381.0	GSM3131265 r1	0:75	A:29202562;C:14935465;G:19738048;T:27228137;N:49363	75	29202562	14935465	19738048	27228137	49363	SRX4041517	SRS3258996	SRA699717	GEO	Molecular Biology, Radboud University	1	0.61061	0.18268	0.87257	0.51994	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48192	48192	SRR7119873	SRX4041516	SRS3258995	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 3dpf mut 42	GSM3131264	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 3dpf mut 42	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	GSM3131264	GSM3131264: Danio rerio RNAseq singleHeart 3dpf mut 42; Danio rerio; RNA Seq	GSM3131264	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131264	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_42_NDCII_sample_0042.fastq.gz	fastq	213129525.0	2841727.0	GSM3131264 r1	0:75	A:66201701;C:36179557;G:46211697;T:64412897;N:123673	75	66201701	36179557	46211697	64412897	123673	SRX4041516	SRS3258995	SRA699717	GEO	Molecular Biology, Radboud University	1	0.62509	0.23068	0.85397	0.4951	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48193	48193	SRR7119872	SRX4041515	SRS3258994	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 3dpf mut 41	GSM3131263	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 3dpf mut 41	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	GSM3131263	GSM3131263: Danio rerio RNAseq singleHeart 3dpf mut 41; Danio rerio; RNA Seq	GSM3131263	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131263	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_41_NDCII_sample_0041.fastq.gz	fastq	166984800.0	2226464.0	GSM3131263 r1	0:75	A:52059221;C:28218639;G:36132669;T:50478431;N:95840	75	52059221	28218639	36132669	50478431	95840	SRX4041515	SRS3258994	SRA699717	GEO	Molecular Biology, Radboud University	1	0.64245	0.22817	0.86535	0.4946	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48194	48194	SRR7119871	SRX4041514	SRS3258992	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 3dpf mut 40	GSM3131262	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 3dpf mut 40	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	GSM3131262	GSM3131262: Danio rerio RNAseq singleHeart 3dpf mut 40; Danio rerio; RNA Seq	GSM3131262	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131262	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_40_NDCII_sample_0040.fastq.gz	fastq	76091325.0	1014551.0	GSM3131262 r1	0:75	A:23961767;C:13365431;G:16139381;T:22578835;N:45911	75	23961767	13365431	16139381	22578835	45911	SRX4041514	SRS3258992	SRA699717	GEO	Molecular Biology, Radboud University	1	0.68263	0.15501	0.86642	0.45686	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48195	48195	SRR7119870	SRX4041513	SRS3258993	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 3dpf mut 39	GSM3131261	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 3dpf mut 39	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	GSM3131261	GSM3131261: Danio rerio RNAseq singleHeart 3dpf mut 39; Danio rerio; RNA Seq	GSM3131261	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131261	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_39_NDCII_sample_0039.fastq.gz	fastq	83697825.0	1115971.0	GSM3131261 r1	0:75	A:25833162;C:14319026;G:18237724;T:25260425;N:47488	75	25833162	14319026	18237724	25260425	47488	SRX4041513	SRS3258993	SRA699717	GEO	Molecular Biology, Radboud University	1	0.68511	0.1681	0.87359	0.50056	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48196	48196	SRR7119869	SRX4041512	SRS3258991	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 3dpf mut 38	GSM3131260	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 3dpf mut 38	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	GSM3131260	GSM3131260: Danio rerio RNAseq singleHeart 3dpf mut 38; Danio rerio; RNA Seq	GSM3131260	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131260	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_38_NDCII_sample_0038.fastq.gz	fastq	89200050.0	1189334.0	GSM3131260 r1	0:75	A:27880894;C:15422868;G:19386687;T:26456153;N:53448	75	27880894	15422868	19386687	26456153	53448	SRX4041512	SRS3258991	SRA699717	GEO	Molecular Biology, Radboud University	1	0.63181	0.17615	0.86736	0.5058	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48197	48197	SRR7119868	SRX4041511	SRS3258989	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 3dpf mut 37	GSM3131259	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 3dpf mut 37	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	GSM3131259	GSM3131259: Danio rerio RNAseq singleHeart 3dpf mut 37; Danio rerio; RNA Seq	GSM3131259	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131259	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_37_NDCII_sample_0037.fastq.gz	fastq	144136050.0	1921814.0	GSM3131259 r1	0:75	A:45236020;C:23884461;G:31356238;T:43570898;N:88433	75	45236020	23884461	31356238	43570898	88433	SRX4041511	SRS3258989	SRA699717	GEO	Molecular Biology, Radboud University	1	0.64128	0.19693	0.86734	0.54791	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48198	48198	SRR7119867	SRX4041510	SRS3258990	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 3dpf mut 36	GSM3131258	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 3dpf mut 36	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	GSM3131258	GSM3131258: Danio rerio RNAseq singleHeart 3dpf mut 36; Danio rerio; RNA Seq	GSM3131258	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131258	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_36_NDCII_sample_0036.fastq.gz	fastq	98485275.0	1313137.0	GSM3131258 r1	0:75	A:31078665;C:16821229;G:21507034;T:29019964;N:58383	75	31078665	16821229	21507034	29019964	58383	SRX4041510	SRS3258990	SRA699717	GEO	Molecular Biology, Radboud University	1	0.62906	0.24825	0.86592	0.56159	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48199	48199	SRR7119866	SRX4041509	SRS3258988	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf mut 35	GSM3131257	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 2dpf mut 35	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2 /	GSM3131257	GSM3131257: Danio rerio RNAseq singleHeart 2dpf mut 35; Danio rerio; RNA Seq	GSM3131257	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131257	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_35_NDCII_sample_0035.fastq.gz	fastq	137582100.0	1834428.0	GSM3131257 r1	0:75	A:42420010;C:23366189;G:30187957;T:41528798;N:79146	75	42420010	23366189	30187957	41528798	79146	SRX4041509	SRS3258988	SRA699717	GEO	Molecular Biology, Radboud University	1	0.69634	0.15154	0.85827	0.50259	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48200	48200	SRR7119865	SRX4041508	SRS3258987	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf mut 34	GSM3131256	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 2dpf mut 34	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2 /	GSM3131256	GSM3131256: Danio rerio RNAseq singleHeart 2dpf mut 34; Danio rerio; RNA Seq	GSM3131256	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131256	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_34_NDCII_sample_0034.fastq.gz	fastq	115231725.0	1536423.0	GSM3131256 r1	0:75	A:36189151;C:19748534;G:25280516;T:33944039;N:69485	75	36189151	19748534	25280516	33944039	69485	SRX4041508	SRS3258987	SRA699717	GEO	Molecular Biology, Radboud University	1	0.65755	0.14147	0.8635	0.53314	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48201	48201	SRR7119864	SRX4041507	SRS3258986	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf mut 33	GSM3131255	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 2dpf mut 33	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2 /	GSM3131255	GSM3131255: Danio rerio RNAseq singleHeart 2dpf mut 33; Danio rerio; RNA Seq	GSM3131255	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131255	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_33_NDCII_sample_0033.fastq.gz	fastq	86985525.0	1159807.0	GSM3131255 r1	0:75	A:27397325;C:14512545;G:19080050;T:25941403;N:54202	75	27397325	14512545	19080050	25941403	54202	SRX4041507	SRS3258986	SRA699717	GEO	Molecular Biology, Radboud University	1	0.63426	0.16676	0.87568	0.5457	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48202	48202	SRR7119863	SRX4041506	SRS3258985	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf mut 32	GSM3131254	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 2dpf mut 32	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2 /	GSM3131254	GSM3131254: Danio rerio RNAseq singleHeart 2dpf mut 32; Danio rerio; RNA Seq	GSM3131254	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131254	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_32_NDCII_sample_0032.fastq.gz	fastq	64224375.0	856325.0	GSM3131254 r1	0:75	A:20154725;C:11180349;G:13983116;T:18869397;N:36788	75	20154725	11180349	13983116	18869397	36788	SRX4041506	SRS3258985	SRA699717	GEO	Molecular Biology, Radboud University	1	0.65978	0.16164	0.8775	0.54741	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48203	48203	SRR7119862	SRX4041505	SRS3258984	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf mut 31	GSM3131253	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 2dpf mut 31	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2 /	GSM3131253	GSM3131253: Danio rerio RNAseq singleHeart 2dpf mut 31; Danio rerio; RNA Seq	GSM3131253	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131253	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_31_NDCII_sample_0031.fastq.gz	fastq	159901350.0	2132018.0	GSM3131253 r1	0:75	A:50993443;C:26156045;G:34865968;T:47792042;N:93852	75	50993443	26156045	34865968	47792042	93852	SRX4041505	SRS3258984	SRA699717	GEO	Molecular Biology, Radboud University	1	0.6343	0.22382	0.84707	0.44037	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48204	48204	SRR7119861	SRX4041504	SRS3258983	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf mut 29	GSM3131252	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 2dpf mut 29	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2 /	GSM3131252	GSM3131252: Danio rerio RNAseq singleHeart 2dpf mut 29; Danio rerio; RNA Seq	GSM3131252	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131252	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_29_NDCII_sample_0029.fastq.gz	fastq	205405950.0	2738746.0	GSM3131252 r1	0:75	A:64163069;C:34538013;G:45210194;T:61373525;N:121149	75	64163069	34538013	45210194	61373525	121149	SRX4041504	SRS3258983	SRA699717	GEO	Molecular Biology, Radboud University	1	0.65436	0.20449	0.84831	0.52226	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48205	48205	SRR7119860	SRX4041503	SRS3258982	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf mut 28	GSM3131251	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 2dpf mut 28	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2 /	GSM3131251	GSM3131251: Danio rerio RNAseq singleHeart 2dpf mut 28; Danio rerio; RNA Seq	GSM3131251	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131251	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_28_NDCII_sample_0028.fastq.gz	fastq	88773525.0	1183647.0	GSM3131251 r1	0:75	A:27560501;C:15646178;G:19351624;T:26163900;N:51322	75	27560501	15646178	19351624	26163900	51322	SRX4041503	SRS3258982	SRA699717	GEO	Molecular Biology, Radboud University	1	0.67182	0.16278	0.86527	0.53604	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48206	48206	SRR7119859	SRX4041502	SRS3258981	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf mut 27	GSM3131250	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 2dpf mut 27	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2 /	GSM3131250	GSM3131250: Danio rerio RNAseq singleHeart 2dpf mut 27; Danio rerio; RNA Seq	GSM3131250	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131250	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_27_NDCII_sample_0027.fastq.gz	fastq	135825300.0	1811004.0	GSM3131250 r1	0:75	A:42874929;C:23016416;G:29588893;T:40267147;N:77915	75	42874929	23016416	29588893	40267147	77915	SRX4041502	SRS3258981	SRA699717	GEO	Molecular Biology, Radboud University	1	0.64606	0.13997	0.86401	0.53196	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48207	48207	SRR7119858	SRX4041501	SRS3258980	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf mut 26	GSM3131249	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 2dpf mut 26	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2 /	GSM3131249	GSM3131249: Danio rerio RNAseq singleHeart 2dpf mut 26; Danio rerio; RNA Seq	GSM3131249	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131249	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_26_NDCII_sample_0026.fastq.gz	fastq	70861500.0	944820.0	GSM3131249 r1	0:75	A:22209781;C:12313683;G:15411508;T:20885853;N:40675	75	22209781	12313683	15411508	20885853	40675	SRX4041501	SRS3258980	SRA699717	GEO	Molecular Biology, Radboud University	1	0.65979	0.17285	0.8687	0.51907	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48208	48208	SRR7119857	SRX4041500	SRS3258979	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 3dpf wt 24	GSM3131248	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 24	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131248	GSM3131248: Danio rerio RNAseq singleHeart 3dpf wt 24; Danio rerio; RNA Seq	GSM3131248	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131248	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_24_NDCII_sample_0024.fastq.gz	fastq	56268825.0	750251.0	GSM3131248 r1	0:75	A:17328594;C:9907009;G:12451765;T:16549368;N:32089	75	17328594	9907009	12451765	16549368	32089	SRX4041500	SRS3258979	SRA699717	GEO	Molecular Biology, Radboud University	1	0.68698	0.13156	0.87647	0.54659	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48209	48209	SRR7119856	SRX4041499	SRS3258978	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 3dpf wt 23	GSM3131247	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 23	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131247	GSM3131247: Danio rerio RNAseq singleHeart 3dpf wt 23; Danio rerio; RNA Seq	GSM3131247	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131247	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_23_NDCII_sample_0023.fastq.gz	fastq	113729700.0	1516396.0	GSM3131247 r1	0:75	A:34708329;C:19742375;G:24997702;T:34216965;N:64329	75	34708329	19742375	24997702	34216965	64329	SRX4041499	SRS3258978	SRA699717	GEO	Molecular Biology, Radboud University	1	0.68965	0.1358	0.86168	0.50041	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48210	48210	SRR7119855	SRX4041498	SRS3258976	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 3dpf wt 22	GSM3131246	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 22	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131246	GSM3131246: Danio rerio RNAseq singleHeart 3dpf wt 22; Danio rerio; RNA Seq	GSM3131246	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131246	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_22_NDCII_sample_0022.fastq.gz	fastq	129788625.0	1730515.0	GSM3131246 r1	0:75	A:39826852;C:22345144;G:28340986;T:39198043;N:77600	75	39826852	22345144	28340986	39198043	77600	SRX4041498	SRS3258976	SRA699717	GEO	Molecular Biology, Radboud University	1	0.68637	0.19709	0.85662	0.52926	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48211	48211	SRR7119854	SRX4041497	SRS3258975	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 3dpf wt 21	GSM3131245	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 21	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131245	GSM3131245: Danio rerio RNAseq singleHeart 3dpf wt 21; Danio rerio; RNA Seq	GSM3131245	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131245	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_21_NDCII_sample_0021.fastq.gz	fastq	74830575.0	997741.0	GSM3131245 r1	0:75	A:23292108;C:12771005;G:16485526;T:22236863;N:45073	75	23292108	12771005	16485526	22236863	45073	SRX4041497	SRS3258975	SRA699717	GEO	Molecular Biology, Radboud University	1	0.62409	0.23647	0.88398	0.52649	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48212	48212	SRR7119853	SRX4041496	SRS3258974	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 3dpf wt 20	GSM3131244	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 20	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131244	GSM3131244: Danio rerio RNAseq singleHeart 3dpf wt 20; Danio rerio; RNA Seq	GSM3131244	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131244	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_20_NDCII_sample_0020.fastq.gz	fastq	83202075.0	1109361.0	GSM3131244 r1	0:75	A:26090654;C:14537361;G:18178302;T:24348215;N:47543	75	26090654	14537361	18178302	24348215	47543	SRX4041496	SRS3258974	SRA699717	GEO	Molecular Biology, Radboud University	1	0.59091	0.18382	0.87274	0.50189	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48213	48213	SRR7119852	SRX4041495	SRS3258973	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 3dpf wt 19	GSM3131243	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 19	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131243	GSM3131243: Danio rerio RNAseq singleHeart 3dpf wt 19; Danio rerio; RNA Seq	GSM3131243	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131243	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_19_NDCII_sample_0019.fastq.gz	fastq	61352025.0	818027.0	GSM3131243 r1	0:75	A:19173237;C:10426603;G:13570586;T:18144746;N:36853	75	19173237	10426603	13570586	18144746	36853	SRX4041495	SRS3258973	SRA699717	GEO	Molecular Biology, Radboud University	1	0.64995	0.19171	0.87213	0.54952	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48214	48214	SRR7119851	SRX4041494	SRS3258972	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 3dpf wt 18	GSM3131242	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 18	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131242	GSM3131242: Danio rerio RNAseq singleHeart 3dpf wt 18; Danio rerio; RNA Seq	GSM3131242	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131242	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_18_NDCII_sample_0018.fastq.gz	fastq	55114425.0	734859.0	GSM3131242 r1	0:75	A:17302961;C:9444084;G:12256958;T:16079162;N:31260	75	17302961	9444084	12256958	16079162	31260	SRX4041494	SRS3258972	SRA699717	GEO	Molecular Biology, Radboud University	1	0.64027	0.2383	0.87903	0.53857	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48215	48215	SRR7119850	SRX4041493	SRS3258971	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 3dpf wt 17	GSM3131241	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 17	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131241	GSM3131241: Danio rerio RNAseq singleHeart 3dpf wt 17; Danio rerio; RNA Seq	GSM3131241	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131241	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_17_NDCII_sample_0017.fastq.gz	fastq	54385575.0	725141.0	GSM3131241 r1	0:75	A:17178884;C:9154385;G:11956346;T:16062768;N:33192	75	17178884	9154385	11956346	16062768	33192	SRX4041493	SRS3258971	SRA699717	GEO	Molecular Biology, Radboud University	1	0.6122	0.27421	0.88552	0.5705	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48216	48216	SRR7119849	SRX4041492	SRS3258970	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 3dpf wt 16	GSM3131240	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 16	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131240	GSM3131240: Danio rerio RNAseq singleHeart 3dpf wt 16; Danio rerio; RNA Seq	GSM3131240	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131240	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_16_NDCII_sample_0016.fastq.gz	fastq	68361225.0	911483.0	GSM3131240 r1	0:75	A:20763268;C:11958924;G:16351810;T:19246084;N:41139	75	20763268	11958924	16351810	19246084	41139	SRX4041492	SRS3258970	SRA699717	GEO	Molecular Biology, Radboud University	1	0.64264	0.12251	0.88477	0.57059	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48217	48217	SRR7119848	SRX4041491	SRS3258969	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 3dpf wt 15	GSM3131239	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 15	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131239	GSM3131239: Danio rerio RNAseq singleHeart 3dpf wt 15; Danio rerio; RNA Seq	GSM3131239	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131239	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_15_NDCII_sample_0015.fastq.gz	fastq	43246350.0	576618.0	GSM3131239 r1	0:75	A:13423239;C:7409151;G:9733956;T:12657584;N:22420	75	13423239	7409151	9733956	12657584	22420	SRX4041491	SRS3258969	SRA699717	GEO	Molecular Biology, Radboud University	1	0.66495	0.14227	0.88828	0.56869	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48218	48218	SRR7119847	SRX4041490	SRS3258968	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf wt 14	GSM3131238	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 2dpf wt 14	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	GSM3131238	GSM3131238: Danio rerio RNAseq singleHeart 2dpf wt 14; Danio rerio; RNA Seq	GSM3131238	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131238	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_14_NDCII_sample_0014.fastq.gz	fastq	81736125.0	1089815.0	GSM3131238 r1	0:75	A:25374411;C:14225355;G:17601172;T:24489651;N:45536	75	25374411	14225355	17601172	24489651	45536	SRX4041490	SRS3258968	SRA699717	GEO	Molecular Biology, Radboud University	1	0.68142	0.17857	0.86965	0.53118	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48219	48219	SRR7119846	SRX4041489	SRS3258967	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf wt 13	GSM3131237	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 2dpf wt 13	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	GSM3131237	GSM3131237: Danio rerio RNAseq singleHeart 2dpf wt 13; Danio rerio; RNA Seq	GSM3131237	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131237	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_13_NDCII_sample_0013.fastq.gz	fastq	62250900.0	830012.0	GSM3131237 r1	0:75	A:19221325;C:10606446;G:13851770;T:18535596;N:35763	75	19221325	10606446	13851770	18535596	35763	SRX4041489	SRS3258967	SRA699717	GEO	Molecular Biology, Radboud University	1	0.67033	0.16463	0.88669	0.52197	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48220	48220	SRR7119845	SRX4041488	SRS3258966	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf wt 12	GSM3131236	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 2dpf wt 12	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	GSM3131236	GSM3131236: Danio rerio RNAseq singleHeart 2dpf wt 12; Danio rerio; RNA Seq	GSM3131236	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131236	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_12_NDCII_sample_0012.fastq.gz	fastq	65079975.0	867733.0	GSM3131236 r1	0:75	A:20574087;C:11008240;G:14305699;T:19155761;N:36188	75	20574087	11008240	14305699	19155761	36188	SRX4041488	SRS3258966	SRA699717	GEO	Molecular Biology, Radboud University	1	0.65516	0.23525	0.87227	0.55436	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48221	48221	SRR7119844	SRX4041487	SRS3258965	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf wt 11	GSM3131235	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 2dpf wt 11	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	GSM3131235	GSM3131235: Danio rerio RNAseq singleHeart 2dpf wt 11; Danio rerio; RNA Seq	GSM3131235	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131235	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_11_NDCII_sample_0011.fastq.gz	fastq	56312400.0	750832.0	GSM3131235 r1	0:75	A:17682751;C:9499488;G:12398396;T:16701718;N:30047	75	17682751	9499488	12398396	16701718	30047	SRX4041487	SRS3258965	SRA699717	GEO	Molecular Biology, Radboud University	1	0.66642	0.21243	0.87868	0.52403	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48222	48222	SRR7119843	SRX4041486	SRS3258964	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf wt 10	GSM3131234	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 2dpf wt 10	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	GSM3131234	GSM3131234: Danio rerio RNAseq singleHeart 2dpf wt 10; Danio rerio; RNA Seq	GSM3131234	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131234	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_10_NDCII_sample_0010.fastq.gz	fastq	51364950.0	684866.0	GSM3131234 r1	0:75	A:16163832;C:8838505;G:11290003;T:15043422;N:29188	75	16163832	8838505	11290003	15043422	29188	SRX4041486	SRS3258964	SRA699717	GEO	Molecular Biology, Radboud University	1	0.65278	0.18749	0.87722	0.53824	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48223	48223	SRR7119842	SRX4041485	SRS3258963	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf wt 9	GSM3131233	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 2dpf wt 9	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	GSM3131233	GSM3131233: Danio rerio RNAseq singleHeart 2dpf wt 9; Danio rerio; RNA Seq	GSM3131233	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131233	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_9_NDCII_sample_0009.fastq.gz	fastq	149036325.0	1987151.0	GSM3131233 r1	0:75	A:47706695;C:23942760;G:33072602;T:44228491;N:85777	75	47706695	23942760	33072602	44228491	85777	SRX4041485	SRS3258963	SRA699717	GEO	Molecular Biology, Radboud University	1	0.56223	0.19674	0.87079	0.52559	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48224	48224	SRR7119841	SRX4041484	SRS3258962	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf wt 8	GSM3131232	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 2dpf wt 8	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	GSM3131232	GSM3131232: Danio rerio RNAseq singleHeart 2dpf wt 8; Danio rerio; RNA Seq	GSM3131232	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131232	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_8_NDCII_sample_0008.fastq.gz	fastq	61857375.0	824765.0	GSM3131232 r1	0:75	A:19180813;C:10701206;G:13569705;T:18368818;N:36833	75	19180813	10701206	13569705	18368818	36833	SRX4041484	SRS3258962	SRA699717	GEO	Molecular Biology, Radboud University	1	0.68869	0.14177	0.86722	0.50808	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48225	48225	SRR7119840	SRX4041483	SRS3258960	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf wt 7	GSM3131231	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 2dpf wt 7	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	GSM3131231	GSM3131231: Danio rerio RNAseq singleHeart 2dpf wt 7; Danio rerio; RNA Seq	GSM3131231	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131231	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_7_NDCII_sample_0007.fastq.gz	fastq	34999125.0	466655.0	GSM3131231 r1	0:75	A:10839927;C:6031095;G:7710789;T:10397147;N:20167	75	10839927	6031095	7710789	10397147	20167	SRX4041483	SRS3258960	SRA699717	GEO	Molecular Biology, Radboud University	1	0.67853	0.1345	0.89727	0.42905	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48226	48226	SRR7119839	SRX4041482	SRS3258959	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf wt 6	GSM3131230	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 2dpf wt 6	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	GSM3131230	GSM3131230: Danio rerio RNAseq singleHeart 2dpf wt 6; Danio rerio; RNA Seq	GSM3131230	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131230	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_6_NDCII_sample_0006.fastq.gz	fastq	53258025.0	710107.0	GSM3131230 r1	0:75	A:16706696;C:9150576;G:11345601;T:16024331;N:30821	75	16706696	9150576	11345601	16024331	30821	SRX4041482	SRS3258959	SRA699717	GEO	Molecular Biology, Radboud University	1	0.6829	0.14834	0.87799	0.49352	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48227	48227	SRR7119838	SRX4041481	SRS3258958	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf wt 5	GSM3131229	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 2dpf wt 5	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	GSM3131229	GSM3131229: Danio rerio RNAseq singleHeart 2dpf wt 5; Danio rerio; RNA Seq	GSM3131229	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131229	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_5_NDCII_sample_0005.fastq.gz	fastq	46391850.0	618558.0	GSM3131229 r1	0:75	A:14186549;C:7964105;G:10302794;T:13910329;N:28073	75	14186549	7964105	10302794	13910329	28073	SRX4041481	SRS3258958	SRA699717	GEO	Molecular Biology, Radboud University	1	0.67937	0.14832	0.88274	0.51203	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48228	48228	SRR7119837	SRX4041480	SRS3258957	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf wt 4	GSM3131228	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 2dpf wt 4	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	GSM3131228	GSM3131228: Danio rerio RNAseq singleHeart 2dpf wt 4; Danio rerio; RNA Seq	GSM3131228	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131228	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_4_NDCII_sample_0004.fastq.gz	fastq	119548650.0	1593982.0	GSM3131228 r1	0:75	A:37089578;C:20710248;G:25820048;T:35861658;N:67118	75	37089578	20710248	25820048	35861658	67118	SRX4041480	SRS3258957	SRA699717	GEO	Molecular Biology, Radboud University	1	0.67925	0.18634	0.84431	0.49844	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48229	48229	SRR7119836	SRX4041479	SRS3258956	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf wt 3	GSM3131227	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 2dpf wt 3	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	GSM3131227	GSM3131227: Danio rerio RNAseq singleHeart 2dpf wt 3; Danio rerio; RNA Seq	GSM3131227	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131227	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_3_NDCII_sample_0003.fastq.gz	fastq	52534500.0	700460.0	GSM3131227 r1	0:75	A:16258360;C:8995544;G:11338397;T:15914972;N:27227	75	16258360	8995544	11338397	15914972	27227	SRX4041479	SRS3258956	SRA699717	GEO	Molecular Biology, Radboud University	1	0.68677	0.14664	0.87541	0.49296	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48230	48230	SRR7119835	SRX4041478	SRS3258955	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 2dpf wt 2	GSM3131226	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 2dpf wt 2	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:2dpf\|genotype:myl7:GFP rnf2+/+	GSM3131226	GSM3131226: Danio rerio RNAseq singleHeart 2dpf wt 2; Danio rerio; RNA Seq	GSM3131226	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131226	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	NDCII_1_2_NDCII_sample_0002.fastq.gz	fastq	27282075.0	363761.0	GSM3131226 r1	0:75	A:8540828;C:4756416;G:5793210;T:8176534;N:15087	75	8540828	4756416	5793210	8176534	15087	SRX4041478	SRS3258955	SRA699717	GEO	Molecular Biology, Radboud University	1	0.689	0.16716	0.89512	0.51016	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Hatching	Embryo	Heart	Cardiovascular System
48231	48231	SRR7119834	SRX4041477	SRS3259001	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 1dpf mut 9	GSM3131225	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 1dpf mut 9	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2 /	GSM3131225	GSM3131225: Danio rerio RNAseq singleHeart 1dpf mut 9; Danio rerio; RNA Seq	GSM3131225	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131225	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	mut_1_9_NDCII_sample_0023.fastq.gz	fastq	57070136.0	762325.0	GSM3131225 r1	0:74.86	A:18605697;C:9652744;G:12793849;T:15973861;N:43985	74	18605697	9652744	12793849	15973861	43985	SRX4041477	SRS3259001	SRA699717	GEO	Molecular Biology, Radboud University	1	0.65648	0.53947	0.94448	0.46511	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Pharyngula	Embryo	Heart	Cardiovascular System
48232	48232	SRR7119833	SRX4041476	SRS3258954	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 1dpf mut 7	GSM3131224	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 1dpf mut 7	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2 /	GSM3131224	GSM3131224: Danio rerio RNAseq singleHeart 1dpf mut 7; Danio rerio; RNA Seq	GSM3131224	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131224	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	mut_1_7_NDCII_sample_0020.fastq.gz	fastq	95756013.0	1278688.0	GSM3131224 r1	0:74.89	A:31571219;C:16875591;G:19112888;T:28125288;N:71027	74	31571219	16875591	19112888	28125288	71027	SRX4041476	SRS3258954	SRA699717	GEO	Molecular Biology, Radboud University	1	0.77787	0.38573	0.89491	0.52033	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Pharyngula	Embryo	Heart	Cardiovascular System
48233	48233	SRR7119832	SRX4041475	SRS3258953	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 1dpf mut 6	GSM3131223	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 1dpf mut 6	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2 /	GSM3131223	GSM3131223: Danio rerio RNAseq singleHeart 1dpf mut 6; Danio rerio; RNA Seq	GSM3131223	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131223	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	mut_1_6_NDCII_sample_0019.fastq.gz	fastq	42326230.0	565166.0	GSM3131223 r1	0:74.89	A:13786789;C:7205959;G:8673068;T:12629903;N:30511	74	13786789	7205959	8673068	12629903	30511	SRX4041475	SRS3258953	SRA699717	GEO	Molecular Biology, Radboud University	1	0.81231	0.24386	0.91662	0.54902	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Pharyngula	Embryo	Heart	Cardiovascular System
48234	48234	SRR7119831	SRX4041474	SRS3258952	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 1dpf mut 5	GSM3131222	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 1dpf mut 5	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2 /	GSM3131222	GSM3131222: Danio rerio RNAseq singleHeart 1dpf mut 5; Danio rerio; RNA Seq	GSM3131222	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131222	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	mut_1_5_NDCII_sample_0018.fastq.gz	fastq	19727283.0	263414.0	GSM3131222 r1	0:74.89	A:6628087;C:3386996;G:3817542;T:5879595;N:15063	74	6628087	3386996	3817542	5879595	15063	SRX4041474	SRS3258952	SRA699717	GEO	Molecular Biology, Radboud University	1	0.77937	0.38158	0.93681	0.49785	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Pharyngula	Embryo	Heart	Cardiovascular System
48235	48235	SRR7119830	SRX4041473	SRS3258951	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 1dpf mut 4	GSM3131221	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 1dpf mut 4	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2 /	GSM3131221	GSM3131221: Danio rerio RNAseq singleHeart 1dpf mut 4; Danio rerio; RNA Seq	GSM3131221	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131221	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	mut_1_4_NDCII_sample_0017.fastq.gz	fastq	58279623.0	778471.0	GSM3131221 r1	0:74.86	A:18649049;C:9706373;G:12497900;T:17382327;N:43974	74	18649049	9706373	12497900	17382327	43974	SRX4041473	SRS3258951	SRA699717	GEO	Molecular Biology, Radboud University	1	0.7618	0.36032	0.91425	0.50881	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Pharyngula	Embryo	Heart	Cardiovascular System
48236	48236	SRR7119829	SRX4041472	SRS3258950	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 1dpf mut 3	GSM3131220	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 1dpf mut 3	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2 /	GSM3131220	GSM3131220: Danio rerio RNAseq singleHeart 1dpf mut 3; Danio rerio; RNA Seq	GSM3131220	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131220	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	mut_1_3_NDCII_sample_0016.fastq.gz	fastq	76875810.0	1027192.0	GSM3131220 r1	0:74.84	A:25047740;C:13094049;G:17143346;T:21533451;N:57224	74	25047740	13094049	17143346	21533451	57224	SRX4041472	SRS3258950	SRA699717	GEO	Molecular Biology, Radboud University	1	0.73765	0.57489	0.91297	0.50116	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Pharyngula	Embryo	Heart	Cardiovascular System
48237	48237	SRR7119828	SRX4041471	SRS3258949	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 1dpf mut 2	GSM3131219	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 1dpf mut 2	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2 /	GSM3131219	GSM3131219: Danio rerio RNAseq singleHeart 1dpf mut 2; Danio rerio; RNA Seq	GSM3131219	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131219	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	mut_1_2_NDCII_sample_0015.fastq.gz	fastq	279841644.0	3736395.0	GSM3131219 r1	0:74.90	A:89952643;C:48371385;G:56655773;T:84653645;N:208198	74	89952643	48371385	56655773	84653645	208198	SRX4041471	SRS3258949	SRA699717	GEO	Molecular Biology, Radboud University	1	0.83707	0.16537	0.8449	0.51435	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Pharyngula	Embryo	Heart	Cardiovascular System
48238	48238	SRR7119827	SRX4041470	SRS3258948	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 1dpf mut 1	GSM3131218	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 1dpf mut 1	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2 /	GSM3131218	GSM3131218: Danio rerio RNAseq singleHeart 1dpf mut 1; Danio rerio; RNA Seq	GSM3131218	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131218	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	mut_1_1_NDCII_sample_0014.fastq.gz	fastq	11439626.0	152750.0	GSM3131218 r1	0:74.89	A:3900812;C:1903149;G:2137242;T:3490826;N:7597	74	3900812	1903149	2137242	3490826	7597	SRX4041470	SRS3258948	SRA699717	GEO	Molecular Biology, Radboud University	1	0.81522	0.22036	0.9427	0.50565	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Pharyngula	Embryo	Heart	Cardiovascular System
48239	48239	SRR7119826	SRX4041469	SRS3258947	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 1dpf wt 11	GSM3131217	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 1dpf wt 11	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2+/+	GSM3131217	GSM3131217: Danio rerio RNAseq singleHeart 1dpf wt 11; Danio rerio; RNA Seq	GSM3131217	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131217	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	W_1_11_NDCII_sample_0013.fastq.gz	fastq	42251524.0	564309.0	GSM3131217 r1	0:74.87	A:13857230;C:6932231;G:9360286;T:12071859;N:29918	74	13857230	6932231	9360286	12071859	29918	SRX4041469	SRS3258947	SRA699717	GEO	Molecular Biology, Radboud University	1	0.73137	0.44634	0.93196	0.46969	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Pharyngula	Embryo	Heart	Cardiovascular System
48240	48240	SRR7119825	SRX4041468	SRS3258946	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 1dpf wt 9	GSM3131216	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 1dpf wt 9	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2+/+	GSM3131216	GSM3131216: Danio rerio RNAseq singleHeart 1dpf wt 9; Danio rerio; RNA Seq	GSM3131216	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131216	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	W_1_9_NDCII_sample_0010.fastq.gz	fastq	140217783.0	1872511.0	GSM3131216 r1	0:74.88	A:48060012;C:23208078;G:28722039;T:40121038;N:106616	74	48060012	23208078	28722039	40121038	106616	SRX4041468	SRS3258946	SRA699717	GEO	Molecular Biology, Radboud University	1	0.80665	0.32237	0.86778	0.52038	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Pharyngula	Embryo	Heart	Cardiovascular System
48241	48241	SRR7119824	SRX4041467	SRS3258945	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 1dpf wt 7	GSM3131215	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 1dpf wt 7	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2+/+	GSM3131215	GSM3131215: Danio rerio RNAseq singleHeart 1dpf wt 7; Danio rerio; RNA Seq	GSM3131215	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131215	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	W_1_7_NDCII_sample_0008.fastq.gz	fastq	23549291.0	314631.0	GSM3131215 r1	0:74.85	A:8015580;C:3998401;G:4892477;T:6623855;N:18978	74	8015580	3998401	4892477	6623855	18978	SRX4041467	SRS3258945	SRA699717	GEO	Molecular Biology, Radboud University	1	0.71017	0.48929	0.94817	0.56724	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Pharyngula	Embryo	Heart	Cardiovascular System
48242	48242	SRR7119823	SRX4041466	SRS3258944	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 1dpf wt 6	GSM3131214	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 1dpf wt 6	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2+/+	GSM3131214	GSM3131214: Danio rerio RNAseq singleHeart 1dpf wt 6; Danio rerio; RNA Seq	GSM3131214	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131214	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	W_1_6_NDCII_sample_0007.fastq.gz	fastq	129689911.0	1732243.0	GSM3131214 r1	0:74.87	A:40869250;C:21297938;G:30638559;T:36786070;N:98094	74	40869250	21297938	30638559	36786070	98094	SRX4041466	SRS3258944	SRA699717	GEO	Molecular Biology, Radboud University	1	0.77101	0.59088	0.88824	0.5086	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Pharyngula	Embryo	Heart	Cardiovascular System
48243	48243	SRR7119822	SRX4041465	SRS3258943	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 1dpf wt 5	GSM3131213	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 1dpf wt 5	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2+/+	GSM3131213	GSM3131213: Danio rerio RNAseq singleHeart 1dpf wt 5; Danio rerio; RNA Seq	GSM3131213	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131213	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	W_1_5_NDCII_sample_0006.fastq.gz	fastq	24218974.0	323441.0	GSM3131213 r1	0:74.88	A:8220059;C:3989695;G:4906493;T:7085365;N:17362	74	8220059	3989695	4906493	7085365	17362	SRX4041465	SRS3258943	SRA699717	GEO	Molecular Biology, Radboud University	1	0.76586	0.49207	0.93501	0.55288	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Pharyngula	Embryo	Heart	Cardiovascular System
48244	48244	SRR7119821	SRX4041464	SRS3258942	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 1dpf wt 4	GSM3131212	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 1dpf wt 4	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2+/+	GSM3131212	GSM3131212: Danio rerio RNAseq singleHeart 1dpf wt 4; Danio rerio; RNA Seq	GSM3131212	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131212	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	W_1_4_NDCII_sample_0005.fastq.gz	fastq	22001311.0	293804.0	GSM3131212 r1	0:74.88	A:7350666;C:3795843;G:4584903;T:6252967;N:16932	74	7350666	3795843	4584903	6252967	16932	SRX4041464	SRS3258942	SRA699717	GEO	Molecular Biology, Radboud University	1	0.7875	0.22891	0.93835	0.52263	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Pharyngula	Embryo	Heart	Cardiovascular System
48245	48245	SRR7119820	SRX4041463	SRS3258941	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 1dpf wt 3	GSM3131211	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 1dpf wt 3	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2+/+	GSM3131211	GSM3131211: Danio rerio RNAseq singleHeart 1dpf wt 3; Danio rerio; RNA Seq	GSM3131211	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131211	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	W_1_3_NDCII_sample_0004.fastq.gz	fastq	113079916.0	1510783.0	GSM3131211 r1	0:74.85	A:37699535;C:19622685;G:23847263;T:31822581;N:87852	74	37699535	19622685	23847263	31822581	87852	SRX4041463	SRS3258941	SRA699717	GEO	Molecular Biology, Radboud University	1	0.76704	0.49567	0.89045	0.51015	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Pharyngula	Embryo	Heart	Cardiovascular System
48246	48246	SRR7119819	SRX4041462	SRS3258977	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 1dpf wt 2	GSM3131210	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 1dpf wt 2	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2+/+	GSM3131210	GSM3131210: Danio rerio RNAseq singleHeart 1dpf wt 2; Danio rerio; RNA Seq	GSM3131210	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131210	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	W_1_2_NDCII_sample_0003.fastq.gz	fastq	28758160.0	384087.0	GSM3131210 r1	0:74.87	A:9200574;C:4647591;G:6808365;T:8081607;N:20023	74	9200574	4647591	6808365	8081607	20023	SRX4041462	SRS3258977	SRA699717	GEO	Molecular Biology, Radboud University	1	0.749	0.43154	0.92498	0.50112	74	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Pharyngula	Embryo	Heart	Cardiovascular System
48247	48247	SRR7119818	SRX4041461	SRS3258961	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively	pubmed:30867528	Danio rerio RNAseq singleHeart 1dpf wt 1	GSM3131209	tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 1dpf wt 1	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:1 dpf\|genotype:myl7:GFP rnf2+/+	GSM3131209	GSM3131209: Danio rerio RNAseq singleHeart 1dpf wt 1; Danio rerio; RNA Seq	GSM3131209	1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131209	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601	W_1_1_NDCII_sample_0002.fastq.gz	fastq	115972945.0	1548390.0	GSM3131209 r1	0:74.90	A:39437412;C:19997472;G:22424748;T:34023469;N:89844	74	39437412	19997472	22424748	34023469	89844	SRX4041461	SRS3258961	SRA699717	GEO	Molecular Biology, Radboud University	1	0.81745	0.22051	0.87746	0.55768	75	B	usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Pharyngula	Embryo	Heart	Cardiovascular System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;