|
| Status |
Public on Sep 10, 2015 |
| Title |
tet-Zscan4 ES cells (Dox+; Zscan4-) |
| Sample type |
SRA |
| |
|
| Source name |
tet-Zscan4c ES cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: tet-Zscan4 Dox+ ES cells
strain: MC1 (129S6/SvEvTac)
chip antibody: 5mC (Eurogentec #BI-MECY-1000)
|
| Treatment protocol |
Zscan4-Flag was repressed in the complete ES medium supplemented with 1.5 µg/ml of Dox, but induced in the absence of Dox.
|
| Growth protocol |
tet-Zscan4c ES cells were cultured on gelatin-coated feeder-free plates in complete ES medium, DMEM (Gibco), 15% FBS (Atlanta Biologicals), 1000 U/ml leukemia inhibitory factor (LIF) (ESGRO, Chemicon), 1 mM sodium pyruvate, 0.1 mM non-essential amino acids (NEAA), 2 mM GlutaMAX, 0.1 mM beta-mercaptoethanol, and penicillin/streptomycin (50 U/50 µg/ml). Medium was changed daily and cells were split every 2 to 3 days routinely.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The genomic DNA isolated from tet-Zscan4c cells (Dox+/Dox-) were randomly sheared by sonication to generate DNA fragments between 300 and 1000 bp. The sonicated DNA (4 μg) was diluted in 450 μl TE, denatured for 10 minutes in boiled water and immediately cooled on ice for 10 minutes. The DNA was incubated with 10 μl of 5mC antibody in 51 μl of 10x IP buffer (100 mM Na-Phosphate pH 7.0, 1.4 M NaCl, 0.5 % Triton X-100) for 2 h at 4°C with shaking. 40 μl of Dynabeads was added to the sample and incubated for 2 hours at 4°C with shaking. The beads were washed with 700 μl of IP buffer for 10 minutes at RT three times, collected with a magnetic rack. After treatment with proteinase K, 5mC-antibody-enriched DNA was extracted and purified.
Library preparation was performed using ChIP-seq sample preparation kit (Illumina). Sequencing analysis was performed on the Illumina Genome Analyzer II according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
5mC Zscan4-
|
| Data processing |
Sequence tags for meDIP experiment were counted in 23946 peak regions identified previously for the H3K27ac chromatin modification. If the peak was shorter than 1 Kb, then the peak region was expanded to 1 Kb to get more sequence tags and enhance the statistical power of analysis. The number of sequence tags was then normalized by the total number of tags.
Genome_build: mm9
Supplementary_files_format_and_content: text
|
| |
|
| Submission date |
Jun 18, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Minoru S.H. Ko |
| E-mail(s) |
kom@mail.nih.gov
|
| Phone |
410-558-8359
|
| Organization name |
NIH
|
| Department |
National Institute on Aging
|
| Lab |
Lab of Genetics
|
| Street address |
251 Bayview Blvd, Suite 100, 10C
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE51682 |
Zscan4 mediates transient remodeling and transcriptional burst of heterochromatin in mouse embryonic stem cells |
| GSE58618 |
Genome-wide DNA methylation analyses by the MeDIP assay |
|
| Relations |
| BioSample |
SAMN02866179 |
| SRA |
SRX610432 |
