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| Status |
Public on Apr 21, 2021 |
| Title |
Chromatin accessibility in D. discoideium (AX4) in different developemental stages [ATAC-seq II] |
| Organism |
Dictyostelium discoideum |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
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.
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| 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
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| Contributor(s) |
Yuan Wang S, Liberman Greer E |
| Citation(s) |
33947439 |
| |
| Submission date |
Jul 02, 2020 |
| Last update date |
Jul 21, 2021 |
| Contact name |
Eric Greer |
| E-mail(s) |
Eric.Greer@childrens.harvard.edu
|
| Organization name |
Boston Children's Hospital/Harvard Medical School
|
| Department |
Newborn Medicine/Department of Pediatrics
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| Lab |
Greer Lab
|
| Street address |
320 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL26000 |
Illumina HiSeq 4000 (Dictyostelium discoideum) |
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| Samples (13)
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| This SubSeries is part of SuperSeries: |
| GSE137604 |
Role of Epigenetics in Unicellular to Multicellular Transition in Dictyostelium |
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| Relations |
| BioProject |
PRJNA643828 |
| SRA |
SRP269799 |
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