NBDC Research ID: hum0266.v1
SUMMARY
Aims: Pemphigus, an autoimmune skin disease, is caused by the production of autoantibodies against desmoglein, an autoantigen. Clinically, treatment targeting B cells has been shown to be effective, and desmoglein-specific B cells may play an important role in the pathogenesis. The purpose of this research is to isolate desmoglein-specific B cells in the peripheral blood of patients using labeled desmoglein protein, and to analyze their characteristics and changes in gene expression due to treatment by comprehensive genetic analysis, and to link them to disease markers and treatments.
Methods: Antigen-specific B cells from PBMCs were single-cell sorted with FACS ARIA3 using labeled desmoglein protein or influenza HA antigen, libraries were prepared with SMART-seq, and sequenced with Novaseq.
Participants/Materials: Desmoglein-specific B cells and non-desmoglein-specific B cells from 3 patients with pemphigus
One of the patients, desmoglein-specific B cells and non-desmoglein-specific B cells after PSL treatment are also included.
Influenza HA specific B cells and non-influenza HA specific B cells from 3 healthy subjects as controls
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000281 | NGS (scRNA-seq) | Controlled-access (Type I) | 2022/12/27 |
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MOLECULAR DATA
| Participants/Materials |
Pemphigus (ICD10: L10.0/L10.2): 3 cases (number of single cells) Desmoglein-specific B cell (37 , 30 , 36) non-desmoglein-specific B cell (44 , 40 , 44) One of the patients, desmoglein-specific B cells and non-desmoglein-specific B cells (31 , 96) after PSL treatment are also included. 3 healthy controls (number of single cells) Influenza HA specific B cell (48 , 36 , 36) non-influenza HA specific B cell (48 , 48 , 48) |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from antigen-specific B cells |
| Cell Lines | - |
| Library Construction (kit name) | SMART-Seq HT Kit |
| Fragmentation Methods | Nextera XT DNA Library Prep Kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000387 |
| Total Data Volume | 200 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shohei Egami
Affiliation: Department of Dermatology, Keio University School of Medicine
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (B) | Elucidating pathophysiology of pemphigus by single cell analysis of auto-reactive B cells | 19H03683 |
| Health and Labor Sciences Research Grants for Research on Rare and Intractable Diseases | Research on rare intractable skin diseases | 20FC1052 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | |||
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
