|
| Status |
Public on Jan 19, 2019 |
| Title |
OA model_Lentiviruses expressing CBX4 rep3 |
| Sample type |
SRA |
| |
|
| Source name |
knee joints
|
| Organism |
Mus musculus |
| Characteristics |
disease state: OA mouse model
tissue: knee joints
treatment: Lentiviruses expressing CBX4
|
| Treatment protocol |
An OA mouse model was generated as previously described. Briefly, anterior cruciate ligament transection (ACLT) was performed on male C57BL/6 mice aged 8 weeks. For the ACLT surgery, after opening the joint capsule, the ACL was transected with microscissors under a surgical micro-scope. One week after surgery, lentiviruses expressing Luc, CBX were injected into the articular cavity. Eight weeks after lentivirus injection, the mice were euthanized and the joints were collected for RNA extraction. The RNA samples of one treatment group were mixed and three technical repeats were performed for RNA-seq.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was extracted using TRIzol (Thermo Fisher Scientific) and genomic DNA was removed using a DNA-free kit (Thermo Fisher Scientific). Quality control and sequencing was done by Novogene Bioinformatics Technology Co.Ltd.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Lentiviruses expressing CBX4
|
| Data processing |
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to mm10 genome using hisat2 software.
Reads were counted by Htseq-count.
Differentially expressed genes were calculated by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: The fomat of processed data is tab seprated file. And, the content is HTseq reads count.
|
| |
|
| Submission date |
Jan 18, 2019 |
| Last update date |
Jan 20, 2019 |
| Contact name |
Zunpeng Liu |
| E-mail(s) |
zunpengliu@163.com
|
| 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 |
GPL21273 |
| Series (1) |
| GSE125320 |
Maintenance of nucleolar homeostasis by CBX4 alleviates senescence and osteoarthritis |
|
| Relations |
| BioSample |
SAMN10769706 |
| SRA |
SRX5261285 |
