|
| Status |
Public on Feb 10, 2021 |
| Title |
mH3K9me3_KO |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow-derived MSCs
|
| Organism |
Mus musculus |
| Characteristics |
cell type: bone marrow-derived MSCs (mBMSCs)
genotype/variation: Prx1Cre; Kdm4bf/f mice (KO)
chip antibody: rabbit anti-H3K9me3 (1:500, Abcam, ab8898, GR3176466-6)
|
| Treatment protocol |
The MSCs were subjected to osteogenic induction (OI) for 4 hours.
|
| Growth protocol |
Both human MSCs and mBMSCs were maintained in DMEM supplemented with 15% FBS and 1% penicillin/streptomycin, repsectively.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP assays were performed using a ChIP assay kit (Upstate Biotechnology, Cat No: 17-295) per the manufacturer's instructions. Briefly, cells were double crosslinked with 10 mM DTBP for 10 min at room temperature, followed by incubation in 1% formaldehyde for 15 min in a 37 °C water bath. Nuclei were extracted and sonication was perfromed to generate 200–500 bp genomic DNA fragments. Chromatin complexes were immunoprecipitated with the related antibodies and Dynabeads Protein A/G. The precipitated DNA was purified using DNA clean and concentrator (Zymo Research).
Libraries were prepared using KAPA Hyper Prep Kit (Kapa Biosystems, Cat No: KK8502)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
The reads were aligned to the hg19/mm9 build of the mouse genome using bowtie.
The sam files were converted into bam files, and then sorted using samtools.
Peak calling was perfromed using MACS2 following the instructions.
Genome_build: hg19/mm9
Supplementary_files_format_and_content: peaks
|
| |
|
| Submission date |
Apr 05, 2020 |
| Last update date |
Feb 11, 2021 |
| Contact name |
Cunyu Wang |
| E-mail(s) |
cwang@dentistry.ucla.edu
|
| Phone |
3108256317
|
| Organization name |
UCLA
|
| Department |
School of Dentistry
|
| Lab |
CHS 56-200
|
| Street address |
10833 Le Conte Ave
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE104257 |
Loss of KDM4B Exacerbates Bone-Fat Imbalance and Mesenchymal Stem Cell Exhaustion in Skeletal Aging [ChIP-seq] |
| GSE104259 |
Loss of KDM4B exacerbates bone-fat imbalance and mesenchymal stromal cell exhaustion in skeletal aging |
|
| Relations |
| BioSample |
SAMN14542036 |
| SRA |
SRX8061039 |
