|
| Status |
Public on Apr 21, 2021 |
| Title |
Streaming stage replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Streaming cell nuclei
|
| Organism |
Dictyostelium discoideum |
| Characteristics |
developmental stage: Streaming
strain: AX4
|
| Growth protocol |
We cultured te strain at 22 °C shaken in the incubator at 180 rpm in HL5 medium with 300 μg/ml streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Frozen pellets of D discoideum cells from the various stages were washed twice with cold PBS and lysed with 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal-630
Nuclei were transposed using the Nextera DNA Library Prep Kit. Transposed libraries were amplified for 11 cycles and size selected for fragments ranging 200-1000 bp. ATAC-seq experiments were sequenced to a minimum depth of 10 million reads/sample.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Real-Time Analysis (RTA) software
The raw fastq files were trimmed for the first and last 8 nucleotides, the multiqc was use to summarize the fastQC results, and the trimmed files were mapped to the Dictyostelium discoideum genome using bowtie2
The mitochondria genome was removed in the alignment process
The duplicated reads were removed by picard and sorted bam files were subject to peak calling with MACS2
Open chromatin regions and peak annotation were deducted with Diffbind and ChIPSeeker, respectively
Genome_build: AX4
Supplementary_files_format_and_content: Peak files for open chromatin regions
|
| |
|
| Submission date |
Sep 17, 2019 |
| Last update date |
Apr 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
|
| Lab |
Greer Lab
|
| Street address |
320 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL26360 |
| Series (2) |
| GSE137598 |
Chromatin accessibility in D. discoideium (AX2) in different developmental stages |
| GSE137604 |
Role of Epigenetics in Unicellular to Multicellular Transition in Dictyostelium |
|
| Relations |
| BioSample |
SAMN12775790 |
| SRA |
SRX6862265 |
