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Accession: PRJNA643828 ID: 643828

Chromatin accessibility in D. discoideium (AX4) in different developemental stages [ATAC-seq II]

See Genome Information for Dictyostelium discoideum
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
AccessionPRJNA643828; GEO: GSE153733
Data TypeEpigenomics
ScopeMultiisolate
OrganismDictyostelium discoideum[Taxonomy ID: 44689]
Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales; Dictyosteliaceae; Dictyostelium; Dictyostelium discoideum
PublicationsWang SY et al., "Role of epigenetics in unicellular to multicellular transition in Dictyostelium.", Genome Biol, 2021 May 4;22(1):134
SubmissionRegistration date: 2-Jul-2020
Greer Lab, Newborn Medicine/Department of Pediatrics, Boston Children's Hospital/Harvard Medical School
RelevanceModel Organism
Project Data:
Resource NameNumber
of Links
Sequence data
SRA Experiments13
Publications
PubMed1
PMC1
Other datasets
BioSample13
GEO DataSets1
GEO Data Details
ParameterValue
Data volume, Supplementary Mbytes2
SRA Data Details
ParameterValue
Data volume, Gbases121
Data volume, Mbytes49409

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