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Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
We apologize for any inconvenience this may cause and appreciate your understanding.

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

JGAD000860

Type of data
NGS (scRNA-seq, bulk RNA-seq, CITE-seq)
Access criteria
Controlled-access (Type I)
Total data volume
2.5 TB
File formats
  • FASTQ
  • HDF5
Research
hum0468
Date published
2025-08-05
Date modified
2025-08-05
DDBJ Search
JGAD000860 (opens in a new tab)
JGA Study
JGAS000727 (opens in a new tab)

Analysis method

scRNA-seq

Materials and participants
rheumatoid arthritis (ICD10: M06.9): 11 cases
blood: 10 samples
joint fluid: 4 samples
synovial membrane: 11 samples (all the type of cells for 3 patients)
healthy controls: 3 individuals
blood: 3 samples
Co-cultures of 1 joint fluid from another rheumatoid arthritis (ICD10: M06.9) patient and blood sample from a control subject: 1sample
  • Health status
    Mixed
  • Subject count
    14 (Individual)
Disease
rheumatoid arthritis (M069)
Sample description
RNAs extracted from CD4+ T cells or sorted all the type of cells of synovial tissues
  • Tissue
    Peripheral blood, Synovial fluid, Synovium
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
scRNA-seq
Target
N/A
Reagent kit
Chromium Single Cell 5'
Fragmentation
included in the above library construction kit
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
500 bp
Reference genome
GRCh38
Mapping
cellranger 7.0.1
QC and filtering
cellranger 7.0.1
Analysis method
cellranger 7.0.1
Gene count
N/A
Data use policy
NBDC data sharing policy (JGAP000001)

RNA-seq

Materials and participants
healthy controls: 1 individual
blood: 1 sample
  • Health status
    Mixed
  • Subject count
    2 (Individual)
Sample description
RNAs extracted from CD4+ T cells isolated from peripheral blood sample or CCR7+ T cells and CXCR6+ T cells isolated from joint fluid samples
  • Tissue
    Peripheral blood, Synovial fluid
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
RNA-seq
Target
N/A
Reagent kit
Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus
Fragmentation
included in the above library construction kit
Platform
Illumina NextSeq 500
Illumina NextSeq 550
Read type
Single-end
Read length
76 bp
Reference genome
GRCh38
Mapping
STAR
QC and filtering
DESeq2
Analysis method
featureCounts
Gene count
N/A
Data use policy
NBDC data sharing policy (JGAP000001)

CITE-seq

Materials and participants
Co-cultures of 1 joint fluid from another rheumatoid arthritis (ICD10: M06.9) patient and blood sample from a control subject: 1sample
  • Health status
    Mixed
  • Subject count
    1 (Sample)
Disease
rheumatoid arthritis (M069)
Sample description
RNAs extracted from CD4+ T cells isolated from tonsil specimens by FACS
  • Tissue
    CD4+ T cell, Cultured cell
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
CITE-seq
Target
N/A
Reagent kit
Chromium Single Cell 5'
Fragmentation
included in the above library construction kit
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
73 bp
Reference genome
GRCh38
Mapping
cellranger 7.0.1
QC and filtering
cellranger 7.0.1
Analysis method
cellranger 7.0.1
Data use policy
NBDC data sharing policy (JGAP000001)