NBDC Research ID: hum0383.v1
SUMMARY
Aims: To elucidate the mechanism and predictors of abatacept, a CTLA4 agonist that regulates T cell co-stimulation, in rheumatoid arthritis (RA) treatment.
Methods: Various peripheral blood immune cell subsets from 5 RA patients were collected (CD16p_Mono, CL_Mono, DN_B, Fr_II_eTreg, mDC, Mem_CD4, Naive_B, Naive_CD4, Neu, NK, pDC, Plasmablast, SM_B, Tfh, Th1, Th17, Th2, USM_B). The patients were analyzed again longitudinally after abatacept treatment. RNA-seq was performed with each immune cell subset sample.
Participants/Materials: 5 RA patients
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000602 | NGS (RNA-seq) | Controlled-access (Type I) | 2023/03/28 |
* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
RA (ICD10: M0690): 5 cases (before/after abatacept treatment) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | Total RNAs extracted from 18 immune cell subsets (CD16p_Mono, CL_Mono, DN_B, Fr_II_eTreg, mDC, Mem_CD4, Naive_B, Naive_CD4, Neu, NK, pDC, Plasmablast, SM_B, Tfh, Th1, Th17, Th2, USM_B) |
| Cell Lines | - |
| Library Construction (kit name) | SMART-seq v4 Ultra Low Input RNA Kit |
| Fragmentation Methods | SMART-seq v4 Ultra Low Input RNA Kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | STAR (hg38) |
| QC Methods | 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 the mean – 2SD were removed. |
| Gene Number | 26353 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000731 |
| Total Data Volume | 17.8 MB (count data, txt) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Keishi Fujio
Affiliation: Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo
Project / Group Name: Analysis of the effect of abatacept for the transcriptome of multiple lymphoid subsets
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Collaborative research fund with Bristol Myers Squibb Japan | Analysis of the effect of abatacept for the transcriptome of multiple lymphoid subsets | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Immunomics analysis of rheumatoid arthritis identified precursor dendritic cells as a key cell subset of treatment resistance | doi: 10.1136/ard-2022-223645 |
JGAD000731 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Shimpei Kubota | Institute for Genetic Medicine, Hokkaido University | Japan | Gene expression and IL-6 amplifying circuit activators in rheumatoid arthritis and systemic lupus erythematosus | JGAD000731 | 2024/02/26-2025/03/31 |
