NBDC Research ID: hum0468.v1
SUMMARY
Aims: The detailed characteristics of the cells present in the local tissues of affected organs are not well understood. Recent advances in analytical techniques have made it possible to analyze cells in human specimens in detail. These analyses have shown, for example, that the gene expression of immune cells in peripheral blood differs from that in tissues, and the importance of analyzing cells in diseased tissues has become clear. This study aims to elucidate the pathophysiology of autoimmune and inflammatory diseases in humans by analyzing the constituent cells and immune cells in affected tissues of autoimmune and inflammatory diseases in detail.
Methods: single-cell RNA-seq, bulk RNA-seq, scASAP-seq, CITE-seq, VDJ-seq, Spacial RNA expression analysis (Xenium)
Participants/Materials:
[scRNA-seq] Blood (10 + 9), joint fluid (4 + 4), and synovial membrane (11 + 10) samples from 11 + 10 rheumatoid arthritis patients, Blood samples from 3 healthy controls, Co-culture of joint fluid (1) from another rheumatoid arthritis patient and blood sample from control subject (1)
[bulk RNA-seq] Joint fluid (1) samples from 1 rheumatoid arthritis patient, Blood samples from 1 healthy controls
[scASAP-seq] Synovial membrane (1) samples from 1 rheumatoid arthritis patient
[CITE-seq] Blood (9), joint fluid (4), and synovial membrane (10) samples from 10 rheumatoid arthritis patients, Co-culture of joint fluid (1) from another rheumatoid arthritis patient and blood sample from control subject (1)
[VDJ-seq] Blood (9), joint fluid (4), and synovial membrane (10) samples from 10 rheumatoid arthritis patients
[Xenium] Synovial membrane (3) samples from 3 rheumatoid arthritis patients
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000727 | NGS (scRNA-seq, bulk RNA-seq, CITE-seq) | Controlled-access (Type I) | 2025/08/01 |
| JGAS000774 | NGS (scRNA-seq, bulk RNA-seq, scASAP-seq, CITE-seq, VDJ-seq), Xenium | Controlled-access (Type I) | 2025/08/01 |
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MOLECULAR DATA
| Participants/Materials |
[JGAS000727] 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 [JGAS000774] rheumatoid arthritis (ICD10: M06.9): 10 cases blood: 9 samples joint fluid: 4 samples synovial membrane: 10 samples
|
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 6000] |
| Library Source | RNAs extracted from CD4+ T cells or sorted all the type of cells of synovial tissues |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 5' Kit |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 500 bp |
| Mapping Methods | cellranger 7.0.1 |
| Reference Genome Sequence | GRCh38 |
| Detecting method for read count (software) | cellranger 7.0.1 |
| QC | cellranger 7.0.1 |
| Gene Number | - |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume |
JGAD000860: 2.5 TB (fastq, h5) JGAD000916: 491.0 GB (fastq, h5) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
[JGAS000727] healthy controls: 1 individual blood: 1 sample [JGAS000774] rheumatoid arthritis (ICD10: M06.9): 1 case joint fluid: 1 sample |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq 500/550] |
| Library Source | RNAs extracted from CD4+ T cells isolated from peripheral blood sample or CCR7+ T cells and CXCR6+ T cells isolated from joint fluid samples |
| Cell Lines | - |
| Library Construction (kit name) |
JGAS000727: Illumina Stranded Total RNA Prep with Ribo-Zero Plus JGAS000774: SMART-Seq mRNA LP |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type |
JGAS000727: Single-end JGAS000774: Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
JGAS000727: 76 bp JGAS000774: 500 bp |
| Mapping Methods | STAR |
| Reference Genome Sequence | GRCh38 |
| Detecting method for read count (software) | featureCounts |
| QC | DESeq2 |
| Gene Number | - |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume |
JGAD000860: 2.5 TB (fastq, h5) JGAD000916: 491.0 GB (fastq, h5) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
rheumatoid arthritis (ICD10: M06.9): 1 case synovial membrane: 1 sample |
| Targets | scATAC-seq + CITE-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Novaseq 6000] |
| Library Source | DNA extracted from CD4+ T cells isolated from samples |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell ATAC Reagent Kits |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 200 bp |
| Mapping Methods | CellRanger ATAC |
| Reference Genome Sequence | GRCh38 |
| Detecting method for open chromatin region (software) | CellRanger ATAC |
| QC Methods | CellRanger ATAC |
| Peak Number | 156,843 peaks |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000916 |
| Total Data Volume | 491.0 GB (fastq, csv) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
[JGAS000727] Co-cultures of 1 joint fluid from another rheumatoid arthritis (ICD10: M06.9) patient and blood sample from a control subject: 1sample [JGAS000774] rheumatoid arthritis (ICD10: M06.9): 10 cases blood: 9 sample joint fluid: 4 samples synovial membrane: 10 samples |
| Targets | CITE-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from CD4+ T cells isolated from tonsil specimens by FACS |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 5' Kit |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 73 bp |
| Software | cellranger 7.0.1 |
| Reference Genome Sequence | GRCh38 |
| Detecting method for read count (software) | cellranger 7.0.1 |
| QC Methods | cellranger 7.0.1 |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume |
JGAD000860: 2.5 TB (fastq, h5) JGAD000916: 491.0 GB (fastq, h5) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
rheumatoid arthritis (ICD10: M06.9): 10 cases blood: 9 cases 9 samples joint fluid: 4 cases 4 samples synovial membrane: 8 cases 10 samples |
| Targets | VDJ-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from CD4+ T cells isolated from samples |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 5' Kit |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 500 bp |
| Japanese Genotype-phenotype Archive Data set ID | JGAD000916 |
| Total Data Volume | 491.0 GB (fastq, tsv) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
rheumatoid arthritis (ICD10: M06.9): 3 cases synovial membrane: 3 samples |
| Targets | Xenium In Situ Gene Expression |
| Target Loci for Capture Methods | 577 genes (multi tissue panel: 377 genes, Custom genes: 100 genes x 2) |
| Platform | 10x Genomics [Xenium v1] |
| Source | synovial membrane samples |
| Cell Lines | - |
| Reagents (Panel, Kit, Version) | Xenium In Situ Gene Expression |
| Software | Xenium Ranger |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000916 |
| Total Data Volume | 491.0 GB (csv, h5, html, json, mtx, tiff, parquet, tsv, xenium, zarr） |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Hiroyuki Yoshitomi
Affiliation: Department of Immunology, Graduate School of Medicine, Kyoto University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Human CD4+ T cells regulate peripheral immune responses in rheumatoid arthritis via insulin-like growth factor like family member 2 | doi: 10.1126/sciimmunol.adr3838 | JGAD000860 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
