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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

JGAD000372

Type of data
NGS (RNA-seq: Systemic sclerosis)
Access criteria
Controlled-access (Type I)
Research
hum0214
Date published
2022-03-16
Date modified
2022-03-16
DDBJ Search
JGAD000372 (opens in a new tab)

Analysis method

RNA-seq

Materials and participants
Systemic Lupus Erythematosus (ICD10: M329): 107 cases
92 healthy controls
  • Health status
    Healthy
Disease
  • Systemic Lupus Erythematosus
Sample description
Total RNAs extracted from 19 immune cell subsets (Naive_CD4, Mem_CD4, Fr._II_eTreg, Th1, Th2, Th17, Tfh, NK, Naive_CD8, Mem_CD8, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CD16n_Mono, CD16p_Mono, mDC, pDC)
Sample provider
N/A
Experimental method
RNA-seq
Target
N/A
Reagent kit
SMART-Seq v4 Ultra Low Input RNA Kit
Smart-seq2
Fragmentation
Smart-Seq v2 for the test cohort and SMART-seq v4 Ultra Low Input RNA Kit for the validation cohort
Platform
Illumina HiSeq 2500
Read type
Paired-end
Read length
76 bp (test cohort)
100 bp (validation cohort)
Reference genome
GRCh38
Mapping
STAR (GRCh38)
QC and filtering
FASTQ files were aligned to the human genome (GRCh38; GenBank assembly GCA_000001405.18) using STAR (v2.5). HTSeq-count (v0.6.1) was used to generate gene counts. In the quality-control analysis, low-quality bases (Phred quality score < 20) were trimmed using the fastx-toolkit (v0.0.14). As the level of mitochondrial transcription is an indicator of cell stress, we applied a cutoff percentage of mitochondrial gene transcripts of < 8%. For detecting outlier samples, Spearman's correlation for each subset was calculated, and samples with an average r2 < 0.8 were omitted as outliers.
Gene count
26,354 (test cohort)
26,485 (validation cohort)
Data use policy
NBDC data sharing policy (JGAP000001)