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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)
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Dataset ID

JGAD000916

Type of data
NGS (scRNA-seq, bulk RNA-seq, scASAP-seq, CITE-seq, VDJ-seq), Xenium
Access criteria
Controlled-access (Type I)
Total data volume
491 GB
File formats
  • FASTQ
  • TBI
  • TXT
  • TSV
  • CSV
  • JSON
  • MTX
  • HDF5
  • TAR
Research
hum0468
Date published
2025-08-05
Date modified
2025-08-05
DDBJ Search
JGAD000916 (opens in a new tab)
JGA Study
JGAS000774 (opens in a new tab)

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0468_target_gene.xlsx577 genes10.6 KB

Analysis method

scRNA-seq

Materials and participants
rheumatoid arthritis (ICD10: M06.9): 10 cases
blood: 9 samples
joint fluid: 4 samples
synovial membrane: 10 samples
  • Health status
    Affected
  • Subject count
    10 (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
rheumatoid arthritis (ICD10: M06.9): 1 case
joint fluid: 1 sample
  • Health status
    Affected
  • Subject count
    1 (Individual)
Disease
rheumatoid arthritis (M069)
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
    Synovial fluid
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
RNA-seq
Target
N/A
Reagent kit
SMART-Seq mRNA LP
Fragmentation
included in the above library construction kit
Platform
Illumina NextSeq 500
Illumina NextSeq 550
Read type
Paired-end
Read length
500 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)

scATAC-seq + CITE-seq

Materials and participants
rheumatoid arthritis (ICD10: M06.9): 1 case
synovial membrane: 1 sample
  • Health status
    Affected
  • Subject count
    1 (Individual)
Disease
rheumatoid arthritis (M069)
Sample description
DNA extracted from CD4+ T cells isolated from samples
  • Tissue
    Synovium
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
CITE-seq
scATAC-seq
Target
N/A
Reagent kit
Chromium Next GEM Single Cell ATAC
Fragmentation
included in the above library construction kit
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
200 bp
Reference genome
GRCh38
Mapping
CellRanger ATAC
QC and filtering
CellRanger ATAC
Analysis method
CellRanger ATAC
Peak count
156,843 peaks
Data use policy
NBDC data sharing policy (JGAP000001)

CITE-seq

Materials and participants
rheumatoid arthritis (ICD10: M06.9): 10 cases
blood: 9 sample
joint fluid: 4 samples
synovial membrane: 10 samples
  • Health status
    Affected
  • Subject count
    10 (Individual)
Disease
rheumatoid arthritis (M069)
Sample description
RNAs extracted from CD4+ T cells isolated from tonsil specimens by FACS
  • Tissue
    Peripheral blood, Synovial fluid, Synovium
  • 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)

VDJ-seq

Materials and participants
rheumatoid arthritis (ICD10: M06.9): 10 cases
blood: 9 cases 9 samples
joint fluid: 4 cases 4 samples
synovial membrane: 8 cases 10 samples
  • Health status
    Affected
  • Subject count
    10 (Individual)
Disease
rheumatoid arthritis (M069)
Sample description
RNAs extracted from CD4+ T cells isolated from samples
  • Tissue
    Peripheral blood, Synovial fluid, Synovium
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
VDJ-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
Data use policy
NBDC data sharing policy (JGAP000001)

Xenium 空間トランスクリプトーム

Materials and participants
rheumatoid arthritis (ICD10: M06.9): 3 cases
synovial membrane: 3 samples
  • Health status
    Affected
  • Subject count
    3 (Individual)
Disease
rheumatoid arthritis (M069)
Sample description
synovial membrane samples
  • Tissue
    Synovium
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
Spatial transcriptomics
Target
577 genes (multi tissue panel: 377 genes, Custom genes: 100 genes x 2)
Reagent kit
Xenium In Situ Gene Expression
Platform
10x Genomics Xenium Analyzer
Analysis method
Xenium Ranger
Data use policy
NBDC data sharing policy (JGAP000001)