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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

JGAD000406

Type of data
NGS (RNA-seq)
Access criteria
Controlled-access (Type I)
Total data volume
173 MB
File formats
  • TXT
Research
hum0214
Date published
2022-01-19
Date modified
2022-01-19
DDBJ Search
JGAD000406 (opens in a new tab)
JGA Study
JGAS000296 (opens in a new tab)

Analysis method

RNA-seq

Materials and participants
Systemic Sclerosis (ICD10: M340): 50 cases
48 healthy controls
(including same cases in E-GEAD-397)
  • Health status
    Healthy
  • Subject count
    98 (Individual)
Disease
  • Systemic Sclerosis
Sample description
Total RNAs extracted from 24 immune cell subsets (Naive_CD4, Mem_CD4, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, Th1, Th2, Th17, Tfh, NK, Naive_CD8, EM_CD8, CM_CD8, TEMRA_CD8, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CL_Mono, Int_Mono, NC_Mono, mDC, pDC)
  • Tissue
    B cell, CD4+ T cell, CD8+ T cell, Dendritic cell, Monocyte, NK cell, Peripheral blood, T cell, Treg cell
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 0.9 were removed.
Gene count
26,353
Processed data type
Count data
Data use policy
NBDC data sharing policy (JGAP000001)