|
| Status |
Public on Apr 24, 2019 |
| Title |
ChIP-DR8dex2_MT-4 |
| Sample type |
SRA |
| |
|
| Source name |
Mesenchymal stem cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: ESC-derived mesenchymal stem cell
genotype: DR8dex2
genotype/variation: transduced with DR8-mtDRBD
|
| Growth protocol |
Human MSCs (hMSCs) derived from hESCs were cultured in MEMa (Thermo Fisher Scientific) medium supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific (Cat:10099-141, Lot:1616964)), 0.1 mM non-essential amino acids (Thermo Fisher Scientific), 1% penicillin/streptomycin (Thermo Fisher Scientific), and 1 ng/mL bFGF (Joint Protein Central, JPC).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using phenol-chloroform-isoamylalcohol extraction and ethanol precipitation.
The H3K9me3 enriched fragments were contructed into libararies via KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series(KK8504) following the manuals.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
H3K9me3 ChIP-seq profile of DR8_dex2 hMSCs transduced with DR8-mtDRBD.
|
| Data processing |
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human refference genome using bowtie2 software.
For peak callling, MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files that we uploaded are MACS2 called peak files. And, all of the processed data files are xls format.
|
| |
|
| Submission date |
Apr 23, 2019 |
| Last update date |
Apr 24, 2019 |
| Contact name |
Zunpeng Liu |
| E-mail(s) |
[email protected]
|
| Phone |
+86 15510715055
|
| Organization name |
State Key Laboratory of Stem Cell and Reproductive Biology
|
| Department |
Institute of Zoology, Chinese Academy of Sciences
|
| Lab |
Jing Qu
|
| Street address |
Beichen West Road
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE130206 |
Stabilizing Heterochromatin by DGCR8 Alleviates Senescence and Osteoarthritis (ChIP-seq) |
|
| Relations |
| BioSample |
SAMN11482805 |
| SRA |
SRX5725703 |
