|
| Status |
Public on Jan 04, 2023 |
| Title |
KO_K27Ac_HiChIP_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
BMDC
|
| Organism |
Mus musculus |
| Characteristics |
cell type: dentritic cells
passages: 8 weeks old
strain: C57BL/6
chip antibody: H3K27ac (Abcam #ab4729)
genotype: CreER;CTCF fl/fl
treatment: none
|
| Treatment protocol |
Bone marrow-derived dendritic cells (BMDCs) were stimulated with LPS at the concentration of 100ng/ml for 3 hours.
|
| Growth protocol |
Bone marrow cells prepared from CreER or CreER;CTCFfl/fl mice were culutred under the presence of murine GM-CSF for 6 days with chaning medium every 2 days. For the deletion of Ctcf allele, 4-OH tamoxifen is added only on the first day of culture.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fixed chromatin was digested using MboⅠ enzyme, followed by biotin incorporation with Biotin-14-dATP. After DNA ligation, the DNA was sonicated and immunoprecipitated with antibody recognizing specific protein. Antibody-chromatin complexed were captured with protein A&G beads. Reverse-crosslinked DNA was captured with Streptavidin C-1 beads.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Purified DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina NovaSeq6000 platform.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Library strategy: Hi-ChIP
Sequenced using Illumina NovaSeq6000 platform
Raw reads were processed using HiC-Pro pipeline v2.11.4 with MBoI restriction sites
Genome_build: mm10
Supplementary_files_format_and_content: hic contaning validpairs
|
| |
|
| Submission date |
Oct 13, 2021 |
| Last update date |
Jan 04, 2023 |
| Contact name |
Hyoung-Pyo Kim |
| E-mail(s) |
kimhp@yuhs.ac
|
| Organization name |
Yonsei University College of Medicine
|
| Department |
Department of Tropical Medicine
|
| Street address |
Yonsei-ro 50-1
|
| City |
Seoul |
| ZIP/Postal code |
03722 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE185883 |
Three-dimensional analysis of genome organization in CTCF-WT and CTCF-KO dendritic cells (HiChIP) |
| GSE185884 |
Three-dimensional analysis of genome organization in CTCF-WT and CTCF-KO dendritic cells |
|
| Relations |
| BioSample |
SAMN22252557 |
| SRA |
SRX12601750 |
