|
| Status |
Public on Oct 04, 2024 |
| Title |
RA-FLS, MTX, biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
rheumatoid arthritis fibroblast-like synoviocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: rheumatoid arthritis fibroblast-like synoviocytes
treatment: methotrexate
|
| Treatment protocol |
Cells were pre-treated for 24 h with 1 uM methotrexate or 2,5 uM tofacitinib or vehicle. They were then stimulated with 2 ng/mL interleukin-1b + 20 ng/mL platelet-derived growth factor in fresh 1% FBS medium with or without the drug for 48 h.
|
| Growth protocol |
Primary rheumatoid arthritis fibroblast-like synoviocytes were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified 5% CO2 atmosphere at 37C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using RNeasy Micro Kit (Qiagen).
Libraries were prepared using TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Data quality assessment was performed using FastQC (0.11.2) and filtering using PRINSEQ (0.20.3).
Reads were mapped to the human reference genome (hg19, UCSC assembly, Feb 2009) using STAR (2.5.2b).
The alignment was sorted and indexed with SAM tools (1.3.1).
Read counts were calculated using HTSeq (0.6.1p1).
Normalization of read counts was performed using DESeq2 size factor method.
Assembly: hg19
Supplementary files format and content: XLSX file includes normalized counts by size factor.
|
| |
|
| Submission date |
Apr 30, 2024 |
| Last update date |
Oct 04, 2024 |
| Contact name |
Anna-Karin Hultgård Ekwall |
| Organization name |
University of Gothenburg
|
| Department |
Rheumatology and Inflammation Research
|
| Street address |
Guldhedsgatan 10A
|
| City |
Gothenburg |
| ZIP/Postal code |
41346 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE266310 |
Effects of methotrexate and tofacitinib on gene expression of activated rheumatoid arthritis fibroblast-like synoviocytes |
|
| Relations |
| BioSample |
SAMN41143283 |
| SRA |
SRX24414585 |
