|
| Status |
Public on Jan 04, 2023 |
| Title |
WT_CTCF |
| Sample type |
SRA |
| |
|
| Source name |
BMDC
|
| Organism |
Mus musculus |
| Characteristics |
cell type: dentritic cells
passages: 8 weeks old
strain: C57BL/6
chip antibody: CTCF (CST #2899)
genotype: CreER
|
| Treatment protocol |
Bone marrow-derived dendritic cells (BMDCs) were stimulated with LPS at the concentration of 100ng/ml for 3 hours. In case of STAT5 ChIP-seq, BMDCs were re-stimulated with GM-CSF for 15 minutes.
|
| 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 cells were sonicated and immunoprecipitated with antibody recognizing specific protein. Antibody-chromatin complexed were captured with protein A&G beads.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Reverse-crosslinked DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina HiSeq2500 platform.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
sequnced using Illumina Hiseq2500 platform
Raw ChIP-seq reads were trimmed for adaptor sequence, and aligned to the mm10 genome assembly using bwa mem v0.7.12 with default parameters
aligned files were filtered for MAPQ > 5 and sorting, deduplication were processed using PICARD v1.77
peaks were called using macs2 v2.1.2 with the following setting: -f BAMPE -g mm (--broad-cutoff 0.1 --broad for H3K27ac,H3K27me3 ChIP-seq peak calling)
normalized abundance file, bigwig files were generated applying CPM normalization using deeptools v3.1.3
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak, broadPeak, CPM normalized bigwig
|
| |
|
| 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 |
GPL17021 |
| Series (2) |
| GSE185880 |
Three-dimensional analysis of genome organization in CTCF-WT and CTCF-KO dendritic cells (ChIP-seq) |
| GSE185884 |
Three-dimensional analysis of genome organization in CTCF-WT and CTCF-KO dendritic cells |
|
| Relations |
| BioSample |
SAMN22252066 |
| SRA |
SRX12601700 |
