NBDC Research ID: hum0393.v1
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SUMMARY
Aims: To explore new biomarkers or therapeutic target molecules using samples from patients with autoimmune diseases
Methods: CD4+CD45RA-CD25hiCD127lo Treg cells were sorted on Moflo XDP cell sorter (Beckman Coulter) from each peripheral blood sample. Total RNA was extracted with TRIZOL-LS (ThermoFisher/Invitrogen) for RNA-seq.
Participants/Materials: Twelve peripheral blood samples were collected from six treatment-naïve rheumatoid arthritis (RA) patients and six healthy individuals.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000693 | NGS (RNA-seq) | Controlled-access (Type I) | 2024/08/23 |
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MOLECULAR DATA
| Participants/Materials |
treatment-naïve rheumatoid arthritis (ICD10: M690): 6 cases (6 samples) 6 healthy individuals (6 samples) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq 500] |
| Library Source | RNAs extracted from CD4+CD45RA-CD25hiCD127lo Treg cells sorted on a cell sorter from each peripheral blood sample |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Ultra II DNA Library Prep Kit, takara smarter kit |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 36 bp x 2 |
| Mapping Methods | CLC Genomics Workbench |
| Reference Genome Sequence | hg19 |
| Detecting method for read count (software) | CLC Genomics Workbench |
| QC | - |
| Gene Number | 57,768 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000826 |
| Total Data Volume | 5.7 GB (fastq, TPM matrix data: csv) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Hiroto Tsuboi
Affiliation: Department of Rheumatology, University of Tsukuba
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (B) | Mechanisms and exhaustion of T follicular regulatory cells in rheumatoid arthritis | 21H02959 |
| establishment of university fellowships towards the creation of science technology innovation, JST | Analysis of age-related changes in regulatory T cell function in rheumatoid arthritis | JPMJFS2106 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Mechanisms of age-related Treg dysfunction in an arthritic environment | doi: 10.1016/j.clim.2024.110337 | JGAD000826 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
