|
| Status |
Public on Jun 04, 2013 |
| Title |
Snf5 moderate digestion |
| Sample type |
SRA |
| |
|
| Source name |
embryonic fibroblast
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6 and 129 mixed
genotype/variation: Snf5-/-
developmental age: E13.5
cell type: Primary mouse embryonic fibroblasts (MEFs)
digetion degree: moderate (4U of Mnase)
|
| Growth protocol |
Primary MEFs were harvested from E13.5 embryos. Cre was introduced into cells via retroviral infection two times at 4-h intervals. Cells were stably selected in medium containing puromycin (2.5 µg/ml) 48 h after infection.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested and nuclei isolated through sucrose gradient. Nuclei were exposed to micrococcal nuclease to release mononucleosome fragments.
The mono-nucleosomal DNA was then isolated, end-repaired, and treated with Taq polymerase to generate a protruding A base for adaptor ligation. After ligation of a pair of Illumina adaptors, the DNA was size selected and amplified by PCR using the adaptor primers. The amplified DNA was then purified and used for cluster generation and sequencing at Illumina instument.
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 5
|
| Data processing |
Sequenced reads were aligned to the mouse genome (mm9) using Bowtie short sequence aligner with default parameters for paired-end reads, reporting only the reads uniquely mapped to the reference genome.
Positions in genome with the numbers of mapped tags above the significance threshold defined by a Z-score of 7 were identified as anomalous and the tags mapped to those positions were discarded.
The fragment frequency at each genome position was calculated for the centers of the paired-end fragments.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files list coordinates of the starts and ends of the DNA fragments retained for the corresponding sample after data filtering. These are plain text files.
|
| |
|
| Submission date |
May 02, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter J Park |
| E-mail(s) |
[email protected]
|
| Phone |
617-432-7373
|
| Organization name |
Harvard Medical School
|
| Department |
Center for Biomedical Informatics
|
| Street address |
10 Shattuck St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE46586 |
The Swi/Snf tumor suppressor complex establishes nucleosome occupancy at target promoters [Mnase-Seq II] |
| GSE46588 |
The Swi/Snf tumor suppressor complex establishes nucleosome occupancy at target promoters |
|
| Relations |
| BioSample |
SAMN02116483 |
| SRA |
SRX273644 |
