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Series GSE104257 Query DataSets for GSE104257
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
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)
GSM4337012 mKDM4B_WT
GSM4337013 mKDM4B_KO
GSM4454172 mH3_WT
This SubSeries is part of SuperSeries:
GSE104259 Loss of KDM4B exacerbates bone-fat imbalance and mesenchymal stromal cell exhaustion in skeletal aging
BioProject PRJNA412202
SRA SRP118897

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Supplementary file Size Download File type/resource
GSE104257_RAW.tar 2.8 Gb (http)(custom) TAR (of BED, BEDGRAPH)
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Raw data are available in SRA
Processed data provided as supplementary file

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