|
| Status |
Public on Jun 25, 2019 |
| Title |
ATAC-SEQ PBS |
| Sample type |
SRA |
| |
|
| Source name |
mouse primary muscle myoblasts
|
| Organism |
Mus musculus |
| Characteristics |
passage: 9-12 passages
age: young adult (6-9week)
strain: C57/BL6
agent: PBS
|
| Treatment protocol |
Cells were treated for 24 hours either with PBS or 5mM DCA
|
| Growth protocol |
Myoblasts were isolated from hindlimb muscles from young adult (6-9week) old C57/BL6 animals, then expanded for ~8 passages prior to experiments.Subconfluent myoblasts (50%) were grown in 15% FBS + DMEM (5mM glucose, 1mM pyruvate, 2mM glutamine) for 24 hours, followed by 24h control or drug treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ATACSeq 50,000 primary myoblasts were prepared according to Buenrostro, et al (Nature Methods, 2013) using the Nextera DNA Library Preparation Kit
Cells were trypsinized and then washed in PBS before downstream processing steps
Sequencing libraries were constructed according to Illumina protocols.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.7
data were aligned against the Mus musculus mm10 genome using BWA (Li,2010)
MACS2 (Zhang, 2008) was used for peak calling
ATAC-seq peaks were further refined as +/–75bp regions of peak summits identified by MACS2.
Common satellite repeat regions were removed against the UCSC Repeatmasker track.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig (.bw)
|
| |
|
| Submission date |
Apr 03, 2019 |
| Last update date |
Jun 26, 2019 |
| Contact name |
Arndt Siekmann |
| Organization name |
UNIVERSITY OF PENNSYLVANIA
|
| Department |
Perelman School of Medicine
|
| Lab |
Arndt Siekmann
|
| Street address |
421 Curie Boulevard, 1114 Biomedical Research Building II/III
|
| City |
PHILADELPHIA |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19103 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE129259 |
Glucose metabolism drives epigenetic landscape transitions that dictate muscle stem cell function |
| GSE129280 |
Muscle stem cell function |
|
| Relations |
| BioSample |
SAMN11322069 |
| SRA |
SRX5628805 |
