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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

E-GEAD-397

Type of data
Read count data from RNA-seq
Access criteria
Unrestricted-access
Total data volume
286 MB
File formats
  • TXT
  • TAR
Research
hum0214
Date published
2021-04-30
Date modified
2021-05-13
DDBJ Search
E-GEAD-397 (opens in a new tab)

Analysis method

RNA-seq

Materials and participants
Systemic Lupus Erythematosus (ICD10: M329): 62 cases
Myositis (ICD10: M339, M332): 65 cases
Systemic Sclerosis (ICD10: M340): 67 cases
Mixed Connective Tissue Disease (ICD10: M351): 19 cases
Sjögren's Syndrome (ICD10: M350): 18 cases
Rheumatoid Arthritis (ICD10: M0690): 25 cases
Behçet's Disease (ICD10: M352): 23 cases
Adult Onset Still's Disease (ICD10: M0610): 18 cases
ANCA-associated Vasculitis (ICD10: M318: 26 cases
Takayasu's Arteritis (ICD10: M314): 16 cases
92 healthy controls
  • Health status
    Mixed
  • Subject count
    431 (Individual)
Disease
  • Systemic Lupus Erythematosus
  • Myositis
  • Systemic Sclerosis
  • Mixed Connective Tissue Disease
  • Sjögren's Syndrome
  • Rheumatoid Arthritis
  • Behçet's Disease
  • Adult Onset Still's Disease
  • ANCA-associated Vasculitis
  • Takayasu's Arteritis
Sample description
Total RNAs extracted from 28 immune cell subsets (Naive_CD4, Mem_CD4, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, Th1, Th2, Th17, Tfh, NK, Naive_CD8, Mem_CD8, EM_CD8, CM_CD8, TEMRA_CD8, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CL_Mono (or CD16n_Mono), CD16p_Mono, Int_Mono, NC_Mono, mDC, pDC, LDG, Neu)
  • Tissue
    Immune cell, 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 HiSeq 2500
Read type
Paired-end
Read length
100 bp
Reference genome
GRCh38
Mapping
STAR (GRCh38)
QC and filtering
From sequenced reads, adaptor sequences were trimmed using cutadapt (v1.16). In addition, 3′- ends with low-quality bases (Phred quality score < 20) were trimmed using the fastx-toolkit (v0.0.14). Reads containing more than 20% low-quality bases were removed. Subsequently, reads were aligned against the GRCh38 reference sequence using STAR (v2.5.3) in two-pass mode with Gencode version 27 annotations. We excluded samples with uniquely mapped read rates < 90% (with the exception of < 70% for plasmablasts and <85% for the other B cell subsets) or unique read counts < 6 × 10^6. Expression was quantified using HTSeq (v 0.11.2.). For QC of the expression data, in each cell population, we filtered low count genes (< 10 in > 90% of samples), normalized between samples with a trimmed mean of M values (TMM) implemented in edgeR software, converted to log-transformed count per million (CPM), removed batch effects using ComBat software and computed inter-sample Spearman's correlations of expression levels between each sample and the remaining samples from the same cell subset. We excluded samples with mean correlation coefficients less than 0.9.
Gene count
53,344
Processed data type
Count data
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)