|
| Status |
Public on Jan 16, 2024 |
| Title |
Synovia of RA patient ST2 |
| Sample type |
SRA |
| |
|
| Source name |
synovia
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: synovia
disease: rheumatoid arthritis
Sex: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from synovial biopsies using the RNeasy kit and an RNase-free DNase set (Qiagen)
Library preparation, QC and 150PE Illumina sequencing services were provided by the external provider Novogene in accordance to the ENCODE guidelines for RNA-Seq (revised version Dec 2016). 30G of data were sequenced per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RA_ST2
|
| Data processing |
The Salmon (v 1.5.2) index was generated using the GRCh38 human genome (GENCODE v38/Ensembl 104) with --type quasi -k 31
Transcript quantification was performed using Salmon (v 1.5.2) with --validateMapping, --useVBOpt and –seqBias
Transcript quantifications were converted to gene-level counts in R using the tximport (v 1.24.0)
DESeq2 (v 1.36.0) was used to correct for library size using “avgTxLength” (normalized_counts)
The “rlog” from DESeq22 (v 1.36.0) for regularised log transformation was used for count transformation (rlog_trnasformed_counts)
Assembly: GRCh38
Supplementary files format and content: Salmon quantification results in .tar format
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Supplementary files format and content: tab-delimited text file include normalized counts for each sample
Supplementary files format and content: tab-delimited text file include rlog transformed counts for each sample
|
| |
|
| Submission date |
Apr 04, 2023 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Hashem Mohammadian |
| Organization name |
University of Erlangen-Nürnberg
|
| Department |
Department of Medicine 3 - Rheumatology and Immunology
|
| Street address |
Ulmenweg 18
|
| City |
Erlangen |
| ZIP/Postal code |
91054 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE228953 |
Molecular reframing of fibroblasts during resolution of arthritis [RNA] |
| GSE228982 |
Molecular reframing of fibroblasts during resolution of arthritis |
|
| Relations |
| BioSample |
SAMN34070589 |
| SRA |
SRX19867698 |
