run_metadata: 49147

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
49147	SRR9962809	SRX6710338	SRS5264193	SRP158893	PRJNA488043	Loss of maternal and zygotic ezh2 reveals the function of Polycomb repression in maintenance of gene expression domain post the body plan is established in zebrafish	GSE119070	Other	The goal of the ChIP sequencing experiments was to assess the differences in occupancy of a selection of chromatin marks and chromatin associated proteins in absence of both maternal and zygotic Ezh2 in zebrafish embryos at 24 hpf. The goal of RNA sequencing experiments was to ass the effect of the absence of both maternal and zygotic Ezh2 on gene expression in zebrafish embryos at 0 3.3 and 24 hpf and link these differences with the changes in epigenetic mark occupancy. Overall design: RNAseq of 0 hph 3.3hpf and 24 hpf Danio rerio wildtype and maternal zygotic ezh2 MZezh2 mutant whole embyos 5 to 7 replicates; ChIPseq for Ezh2 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for H3K27me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for Rnf2 in 24 hpf Danio rerio wildtype 1 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K4me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K27ac in 24 hpf Danio rerio wildtype 3 replicates and MZezh2 mutant 3 sample whole embryos;		pubmed:31488564		RNAseq MZezh2mutant 0hpf rep6	GSM4030411		tissue:RNAseq MZezh2mutant 0hpf\|strain background:TU/TLF mixed background\|genotype/variation:MZezh2 / \|age:0 hpf embryo	RNAseq MZezh2mutant 0hpf rep6	RNA seq: reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Genome build: GRCz10 Supplementary files format and content: Raw gene counts .tab	RNAseq MZezh2mutant 0hpf		RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples 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 background:TU/TLF mixed background\|genotype/variation:MZezh2 / \|age:0 hpf embryo	GSM4030411	GSM4030411: RNAseq MZezh2mutant 0hpf rep6; Danio rerio; RNA Seq	GSM4030411		1	RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP158893			RNAseq_MZezh2mutant_0hpf_rep6_R1.fastq.gz RNAseq_MZezh2mutant_0hpf_rep6_R2.fastq.gz	fastq fastq	1818269208.0	21646062.0	GSM4030411 r1	0:42 1:42	A:467737566;C:434429557;G:451696449;T:463995685;N:409951	42	42			467737566	434429557	451696449	463995685	409951	SRX6710338	SRS5264193	SRA763417	GEO	Molecular Biology, Radboud University	2	0.63664	0.64501	0.1054	0.101	0.73736	0.73937	0.47347	0.47482	42	42	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	ribozero	bulk	unknown	unknown		Netherlands	2019-08-13	Zygote	Embryo	Whole Organism	All anatomical structures