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Series GSE114038 Query DataSets for GSE114038
Status Public on Mar 13, 2019
Title The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis
Organism Danio rerio
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary 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 and 3 dpf Danio rerio dissected hearts, wild types (9, 13 and 10 replicates, respectively) and rnf2 mutants (8, 9 and 9 replicates, respectively)
 
Contributor(s) Chrispijn ND, Elurbe DM, Aben M, de Bakker D, Bakkers J, Kamminga LM
Citation(s) 30867528
Submission date May 04, 2018
Last update date Mar 28, 2019
Contact name Leonie M Kamminga
E-mail(s) leonie.kamminga@wur.nl
Organization name Radboud University
Department Molecular Biology
Street address Geert Grooteplein 28
City Nijmegen
ZIP/Postal code 6525 GA
Country Netherlands
 
Platforms (2)
GPL14875 Illumina HiSeq 2000 (Danio rerio)
GPL20828 Illumina NextSeq 500 (Danio rerio)
Samples (85)
GSM3131182 Danio_rerio_RNAseq_3dpf_wt1
GSM3131183 Danio_rerio_RNAseq_3dpf_wt2
GSM3131184 Danio_rerio_RNAseq_3dpf_wt3
Relations
BioProject PRJNA459724
SRA SRP144601

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE114038_RAW.tar 3.8 Mb (http)(custom) TAR (of BED, TXT)
GSE114038_singleHearts_monocle_1dpf_2sd_expressedGenes_normCounts.txt.gz 211.5 Kb (ftp)(http) TXT
GSE114038_singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt.gz 568.0 Kb (ftp)(http) TXT
GSE114038_singleHearts_monocle_3dpf_2sd_expressedGenes_normCounts.txt.gz 496.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file
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