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Genome Information for Dictyostelium discoideum
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4 additional projects are components of the Role of Epigenetics in Unicellular to Multicellular Transition in Dictyostelium.
The goal of ATAC-seq is to identify the open chromatin regions in the wild-type D.discoideum at different developmental stages (vegetative, streaming, mound and fruiting bodyies). Three biological replicates were assigned for each group and in total 13 groups were prepared for ATAC-seq libraries. We mapped about 30 million reads per sample to D. discoideum with bowtie2 workflow. Open chromatin regions were deducted by ChIPseeker with corrected p < 0.05. Our results showed D. discoideum have dispartate chromatin accessibility regions throughout the genome.
Overall design: Fresh nuclei from vegetative, streaming, mound and fruiting body stages were extacted and transposed, and cDNA libraries were generated for deep sequencing, in triplicate, using Hiseq 4000
| Accession | PRJNA643828; GEO: GSE153733 |
| Data Type | Epigenomics |
| Scope | Multiisolate |
| Organism | Dictyostelium discoideum[Taxonomy ID: 44689] Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales; Dictyosteliaceae; Dictyostelium; Dictyostelium discoideum |
| Publications | Wang SY et al., "Role of epigenetics in unicellular to multicellular transition in Dictyostelium.", Genome Biol, 2021 May 4;22(1):134 |
| Submission | Registration date: 2-Jul-2020
Greer Lab, Newborn Medicine/Department of Pediatrics, Boston Children's Hospital/Harvard Medical School |
| Relevance | Model Organism |
Project Data:
| Resource Name | Number
of Links |
|---|
| Sequence data |
| SRA Experiments | 13 |
| Publications |
| PubMed | 1 |
| PMC | 1 |
| Other datasets |
| BioSample | 13 |
| GEO DataSets | 1 |