|
| Status |
Public on Apr 21, 2021 |
| Title |
ATAC-seq_Mound stage replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Mound cell nuclei
|
| Organism |
Dictyostelium discoideum |
| Characteristics |
developmental stage: Mound
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 |
Dictyostelium were physically dissociated and washed twice with PBS with 0.04% BSA and lysed with 10 mM Tris-HCL (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.5% Tween 20, 0.5% NP-50, 0.05% digitonin (Promega G944A), 1% BSA, and 0.5% cellulase on ice or room temperature for 30 minutes to fully lyse the cells. Validation of equivalent ATACseq lysine of different stages was performed by trypan blue staining and optimized by real-time PCR detection of ribosomal RNA release.
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 25 million reads/sample.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Real-Time Analysis (RTA) software
The raw fastq files were trimmed for the adaptor sequences, 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
The bam files were shifted for +4bp and -5bp for positive and negative strand, respectively
The 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 |
Jul 02, 2020 |
| 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 |
GPL26000 |
| Series (2) |
| GSE137604 |
Role of Epigenetics in Unicellular to Multicellular Transition in Dictyostelium |
| GSE153733 |
Chromatin accessibility in D. discoideium (AX4) in different developemental stages [ATAC-seq II] |
|
| Relations |
| BioSample |
SAMN15430172 |
| SRA |
SRX8658224 |
