|
| Status |
Public on Sep 10, 2019 |
| Title |
soleus_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
skeletal muscle - soleus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: wild type
tissue: skeletal muscle - soleus
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Skeletal muscle was dissected and snap frozen in liquid nitrogen. ATAC-seq samples were cryo-pulverized and 30mg of powdered tissue was subjected to transposase reaction as per Buenrostro et al 2013.
ATAC-seq libraries were prepared as per Beunrostro et al 2013.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Soleus-pooled_S4
|
| Data processing |
Alignment: Paired end sequence reads were obtained and mapped to the mouse mm10 genome using Bowtie 2.
Peaks: Tag directories were generated in HOMER using the -tbp 1 command to remove clonal reads. Peaks were identified with Homer findPeaks using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text (txt) files with annotated peak lists, and bedgraphs
|
| |
|
| Submission date |
Jul 26, 2019 |
| Last update date |
Sep 10, 2019 |
| Contact name |
Grant D. Barish |
| Organization name |
Northwestern University
|
| Department |
Medicine
|
| Street address |
303 E Superior Street
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE123879 |
Enhancer Profiling Reveals Regulators of Skeletal Muscle Identity and Reprogramming |
| GSE134962 |
Enhancer Profiling Reveals Regulators of Skeletal Muscle Identity and Reprogramming [ATAC-seq] |
|
| Relations |
| BioSample |
SAMN12375416 |
| SRA |
SRX6601509 |
