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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

JGAD000603

Type of data
NGS (RNA-seq)
Access criteria
Controlled-access (Type I)
Total data volume
478 MB
File formats
  • TXT
Research
hum0214
Date published
2022-08-24
Date modified
2022-08-24
DDBJ Search
JGAD000603 (opens in a new tab)
JGA Study
JGAS000486 (opens in a new tab)

Analysis method

RNA-seq

Materials and participants
Systemic Lupus Erythematosus (ICD10: M329): 136 cases
(22 SLE patients were analyzed longitudinally, total 159 samples)
89 healthy controls
  • Health status
    Healthy
Disease
  • Systemic Lupus Erythematosus
Sample description
Total RNAs extracted from 27 immune cell subsets (Naive_CD4, Mem_CD4, Th1, Th2, Th17, Tfh, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, Naive_CD8, EM_CD8, CM_CD8, TEMRA_CD8, NK, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CL_Mono (or CD16n_Mono), CD16p_Mono, Int_Mono, NC_Mono, mDC, pDC, Neu, LDG)
  • Tissue
    Peripheral blood
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
Illumina NovaSeq 6000
Read type
Paired-end
Read length
100 bp (HiSeq 2500)
150 bp (NovaSeq 6000)
Reference genome
GRCh38
Mapping
STAR (GRCh38)
QC and filtering
Adaptor sequences were trimmed using Cutadapt and reads containing low-quality bases (Phred quality score < 20 in > 20% of the bases) were removed. Reads were aligned to the human genome within the UCSC Genome Browser (GRCh38) using STAR, and expression was counted with HTSeq. Samples with uniquely mapped read rates < 80% or unique read counts < 5 × 10⁶ were excluded. We calculated Spearman's correlations of the expressions between two samples from the same cell type and then removed the samples with mean correlation coefficients < 0.9. In addition, samples with the concordance rates between RNA-seq-based genotype and WGS-based genotype at the heterozygous loci < 0.9 were excluded.
Gene count
26,353
Processed data type
Count data
Data use policy
NBDC data sharing policy (JGAP000001)