|
| Status |
Public on Dec 22, 2021 |
| Title |
Primary chondrocytes - mutant FLAG-SP7 |
| Sample type |
SRA |
| |
|
| Source name |
Primary chondrocytes
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse primary chondrocytes
strain: C57BL/6
chip antibody: FLAG M2 antibody (Sigma, F1804)
|
| Treatment protocol |
On the day of infection, the retrovirus-containing cell culture media (produced by transfecting ECO cells with retroviral plasmids) were filtered with a 0.45um membrane filter, mixed 1:1 with full chondrocyte, and supplemented with 8ug/ml polybrene. Chondrocytes infected twice with the media (once in the morning and second time overnight or longer). Successful retroviral infection was indicated by GFP signal in cells after incubation (close to 100% infection efficiency).
|
| Growth protocol |
Primary mouse chondrocytes isolated from proximal tibia and distal femur of 7 day old male mice cardiomyocytes were cultured in DMEM/F12 media supplemented with 10% FBS, P/S, and 50 μg/mL ascorbic acid at 37C and 5% CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Protein-DNA complexes were crosslinked with 1% formaldehyde, Lysates were clarified from sonicated nuclei and Protein-DNA complexes were purified with FLAG antibody.
SMARTer ThruPLEX DNA-seq Kit (R400428, Takara Bio)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Fastq files were trimed by Trimmomatic-0.33 with follwing options: LEADING:20 TRAILING:20 MINLEN:50 CROP:50 HEADCROP:10
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie 1.2.2 with follwing options: -v 2 -m 1
Peak calling was performed by two-sample analysis on CisGenome software (Ji et al., 2008) with a P-value cutoff of 10-5 comparing with the input control
Genome_build: mm9
Supplementary_files_format_and_content: peak bed file
|
| |
|
| Submission date |
May 26, 2020 |
| Last update date |
Dec 22, 2021 |
| Contact name |
Hironori Hojo |
| E-mail(s) |
hojo@tetrapod.t.u-tokyo.ac.jp
|
| Phone |
+81-3-5841-1427
|
| Organization name |
The University of Tokyo
|
| Department |
Center for Disease Biology and Integrative Medicine
|
| Lab |
Clinical Biotechnology
|
| Street address |
7-3-1 Hongo
|
| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
113-8655 |
| Country |
Japan |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE151217 |
The effect of S309W mutation on SP7 genomic binding in chondrocytes |
|
| Relations |
| BioSample |
SAMN15020662 |
| SRA |
SRX8401625 |
