|
Status |
Public on Jan 16, 2024 |
Title |
Synovia of RA patient ST8 |
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_ST8
|
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 |
SAMN34070584 |
SRA |
SRX19867704 |