 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 10, 2021 |
| Title |
Loss of KDM4B Exacerbates Bone-Fat Imbalance and Mesenchymal Stem Cell Exhaustion in Skeletal Aging [ChIP-seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Mesenchymal stem/stromal cells (MSCs) are multipotent progenitor cells with multilineage differentiation potentials. We previously reported histone demethylases KDM4B promoted osteogenesis and inhibited adipogenesis of human MSCs. To identify genome-wide enrichments of KDM4B and the changes in H3K9me3 marks when loss of KDM4B, Primary MSCs were isolated from Prx1Cre; Kdm4bf/f mice and control mice. ChIP-seq assay was performed using KDM4B, H3K9me3 and H3 antibody, respectively.
|
| |
|
| Overall design |
Identification of genome-wide enrichments of KDM4B and H3K9me3 marks in mouse bone marrow-derived MSCs.
Primary mMSCs were isolated from Prx1Cre; Kdm4bf/f mice (KO) and Prx1Cre; Kdm4bw/w mice (WT).
ChIP assay was performed using KDM4B, H3K9me3 and H3 antibody (rabbit anti-KDM4B (1:400, Bethyl Laboratories, Cat No: A301-478A, Lot No.: 2); rabbit anti-KDM4B (1:400, Abcam, Cat No: ab191434, Lot No.: EPR18603-2); rabbit anti-H3K9me3 (1:500, Abcam, Cat No: ab8898, Lot No.: GR3176466-6) and rabbit anti-H3 (1:200, Cell Signaling Technology, Cat#2650, Lot No.: 20)), , respectively. Yeast chromatin was added as a spike-in control for H3K9me3 ChIP-seq. Libraries were prepared using KAPA Hyper Prep Kit (Kapa Biosystems, KK8502) per the manufacturer’s protocol. The sequencing was completed using HiSeq 3000 system (Illumina) or Nextseq 500 at the Technology Center for Genomics & Bioinformatics (TCGB) of UCLA.
|
| |
|
| Contributor(s) |
Deng P, Su T, Wang J, Wang C |
| Citation(s) |
33571444 |
| Submission date |
Sep 26, 2017 |
| Last update date |
May 12, 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 |
| |
|
| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL21493 |
Illumina HiSeq 3000 (Mus musculus) |
|
| Samples (8)
|
|
| This SubSeries is part of SuperSeries: |
| GSE104259 |
Loss of KDM4B exacerbates bone-fat imbalance and mesenchymal stromal cell exhaustion in skeletal aging |
|
| Relations |
| BioProject |
PRJNA412202 |
| SRA |
SRP118897 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE104257_RAW.tar |
2.8 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...