|
| Status |
Public on Apr 18, 2024 |
| Title |
DBA_CIA_c |
| Sample type |
SRA |
| |
|
| Source name |
synovial membrane
|
| Organism |
Mus musculus |
| Characteristics |
tissue: synovial membrane
strain: DBA/1
genotype: collagen-induced-arthritis (CIA)
treatment: regular diet
|
| Treatment protocol |
To further investigate whether obesity influences RA, we established collagen-induced-arthritis (CIA) models in mice using both regular and high-fat diets (HFD), and collected synovial tissue and performed RNA sequencing.
|
| Growth protocol |
Mice were fed with regular diets
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted from synovial membrane. The samples were homogenized in Trizol (Invitrogen) and processed for RNA extraction according to the manufacturer’s instructions.
BGI in-house kit (BGI-Shenzhen, China)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
Raw sequencing reads (fastq) were quality checked using SOAPnuke (v1.5.2).
Bowtie2 (v2.2.5) was applied to align the clean reads to the genomes.
The expression level of gene was calculated by RSEM (v1.2.12).
Differential expression analysis was performed using DESeq2 (v1.4.5)
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: core_table_gene2.xls
|
| |
|
| Submission date |
Feb 28, 2024 |
| Last update date |
Apr 18, 2024 |
| Contact name |
jianhui liang |
| E-mail(s) |
jh.liang@siat.ac.cn
|
| Organization name |
Shenzhen Institute of Science and Technology
|
| Street address |
1068 Xueyuan Avenue, Nanshan District
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518000 |
| Country |
China |
| |
|
| Platform ID |
GPL28457 |
| Series (1) |
| GSE260460 |
Body mass index alone may not serve as a reliable indicator of the risk of developing rheumatoid arthritis |
|
| Relations |
| BioSample |
SAMN40188342 |
| SRA |
SRX23778939 |
