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Sample GSM8117694 Query DataSets for GSM8117694
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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