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We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

JGAD000731

Type of data
NGS (RNA-seq)
Access criteria
Controlled-access (Type I)
Total data volume
17.8 MB
File formats
  • TXT
Research
hum0383
Date published
2023-03-27
Date modified
2023-03-27
DDBJ Search
JGAD000731 (opens in a new tab)
JGA Study
JGAS000602 (opens in a new tab)

Analysis method

RNA-seq

Materials and participants
RA (ICD10: M0690): 5 cases
(before/after abatacept treatment)
  • Health status
    Affected
  • Subject count
    5 (Individual)
Disease
  • RA
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)
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
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 NovaSeq 6000
Read type
Paired-end
Read length
150 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)