Dataset ID
JGAD000727
- Type of data
- NGS (RNA-seq)
- Access criteria
- Controlled-access (Type I)
- Total data volume
- 114 MB
- File formats
- TXT
- Research
- hum0214
- Date published
- 2023-03-28
- Date modified
- 2023-03-28
- DDBJ Search
- JGAD000727 (opens in a new tab)
- JGA Study
- JGAS000598 (opens in a new tab)
Analysis method
RNA-seq
- Materials and participants
- Rheumatoid Arthritis (ICD10: M0690): 50 cases
(15 RA patients were analyzed longitudinally)
39 healthy controls
(including same cases in E-GEAD-397) - Health statusHealthy
- Subject count89 (Individual)
- Disease
- Rheumatoid Arthritis
- Sample description
- Total RNAs extracted from 18 immune cell subsets (CD16p_Mono, CL_Mono, DN_B, Fr_II_eTreg, mDC, Mem_CD4, Naive_B, Naive_CD4, Neu, NK, pDC, Plasmablast, SM_B, Tfh, Th1, Th17, Th2, USM_B)
- Sample provider
- N/A
- Experimental method
- RNA-seq
- Target
- N/A
- Reagent kit
- SMART-Seq v4 Ultra Low Input RNA Kit
- Fragmentation
- SMART-seq v4 Ultra Low Input RNA Kit
- Platform
- Illumina HiSeq 2500
- Read type
- Paired-end
- Read length
- 100 bp
- Reference genome
- GRCh38
- Mapping
- STAR (hg38)
- QC and filtering
- The adaptor sequences and 3' low quality bases (Phred quality score < 20) were trimmed. Short reads (< 50bp) and reads containing many low quality bases (Phred quality score < 20 in > 20% of the bases) were removed. If the uniquely mapped rate was less than 80%, or the number of uniquely mapped reads was 5.00 x 10⁶ reads, the sample was removed before further analysis. The correlation coefficient of the expression data between two samples belonging to the same cell subset and calculated the average of the correlation coefficient (Di). Samples for which Di was less than the mean - 2SD were removed.
- Gene count
- 26,353
- Processed data type
- Count data
- Data use policy
- NBDC data sharing policy (JGAP000001)