|
| Status |
Public on Apr 19, 2016 |
| Title |
Oct4 ChIP-Seq at G1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic stem cells (E14)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
chip antibody: Oct4 (Santa Cruz, sc-5279)
phase: G1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cross-linked with 1% (v/v) formaldehyde for 5 minutes at 37℃ and lysed. Then, nuclear pellets were sheared with Focused-ultrasonicator (Covaris) and immunoprecipitated. The immune complexes were eluted by adding 250ul of elution buffer containing 1% (w/v) SDS and 0.1M NaHCO3 two times. Cross-linking was reversed by adding of 20ul of 5M NaCl and incubated overnight at 65C. DNA was precipitated with ethanol and kept in -20℃ for the further use.
The immunoprecipitated (20ng/μL) samples were used for library preparation for Illumina sequencing using the TruSeq ChIP kit (Illumina, San Diego, CA) following the manufacturer's protocol. Briefly, 20 ng of immunoprecipitated DNA samples was end repaired-ligated to Illumina adaptors and selected for a fragment size of approximately 300 bp by gel extraction. Multiplex Illumina primers were used to amplify gel-extracted products.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
nocodazole treated for 10 hours
|
| Data processing |
Reads after sequencing were mapped against to the mouse genome using Bowtie 2 version 2.2.6.
The outputs were sorted by Picard tools and reliable reads based on mapping score were used in subsequent processes.
We used MACS v.1.4.2 tool to select binding sites of Oct4 with default setting.
TDF files were generated by using the igvtools package.
Genome_build: mm9
Supplementary_files_format_and_content: tdf
|
| |
|
| Submission date |
Feb 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jihoon Shin |
| E-mail(s) |
sjhuu@snu.ac.kr
|
| Organization name |
Seoul National University College of Medicine
|
| Street address |
Biomedical Science Building, 103 Daehakro, Jongro-gu
|
| City |
Seoul |
| ZIP/Postal code |
110-799 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE78073 |
Oct4 ChIP-Seq at G1 and G2/M phase of cell cycle in mouse embryonic stem cells |
|
| Relations |
| SRA |
SRX1592541 |
| BioSample |
SAMN04503060 |
