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Sample GSM4454175 Query DataSets for GSM4454175
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
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
BioSample SAMN14542036
SRA SRX8061039

Supplementary file Size Download File type/resource
GSM4454175_mH3K9me3_KO_new.bed.gz 432.0 Kb (ftp)(http) BED
GSM4454175_mH3K9me3_KO_new.bedGraph.gz 156.2 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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