NBDC Research ID: hum0416.v3
SUMMARY
Aims: In order to grasp the biological reactions and pathological conditions occurring in the body in more detail for diseases involving immune reactions, blood and tissue samples were used and analyzed by following the changes and changes over time for each patient. The present research will acquire and profile comprehensive parameters for each patient and explore factors related to disease conditions and treatments. Then, it will be linked to the understanding of pathology and the development of therapeutic methods through the confirmation of changes in the found molecules and the search for functions.
Methods: single-cell CITE-seq (Cellular indexing of transcriptomes and epitopes), BD Ab-seq
Participants/Materials: microscopic polyangiitis (MPA), systemic sclerosis (SSc), healthy donors
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| E-GEAD-635 | NGS (CITE-seq) | Unrestricted-access | 2023/08/10 |
| DRA019233 | NGS (BD Ab-seq) | Unrestricted-access | 2024/09/27 |
| E-GEAD-867 | NGS (BD Ab-seq) | Unrestricted-access | 2024/09/27 |
| DRA019274 | NGS (CITE-seq, BD Ab-seq) | Unrestricted-access | 2024/10/16 |
| E-GEAD-872 | NGS (CITE-seq, BD Ab-seq) | Unrestricted-access | 2024/10/16 |
*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more
MOLECULAR DATA
| Participants/Materials |
[E-GEAD-635] microscopic polyangiitis (ICD10: M31.7): 8 cases blood samples were collected from 3 patients twice and 5 patients once 7 healthy donors [DRA019274 / E-GEAD-872] systemic sclerosis (ICD10: M34): 21 cases blood samples were collected from a patient three times and 20 patients once 6 healthy donors (3 are also used in E-GEAD-635) |
| Targets | CITE-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500, NovaSeq 6000] |
| Library Source | RNAs extracted from a single cell isolated from PBMCs |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Single Cell 5' Reagent Kits v2 |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 91 bp |
| Software | CellRanger (version 6.0.6) |
| Reference Genome Sequence | GRCh38 |
| QC Methods | Cell Ranger Metrics |
| DDBJ Sequence Read Archive ID | DRA019274 |
| Genomic Expression Archive ID | |
| Total Data Volume |
E-GEAD-635: 311 MB (expression matrix, HDF5) DRA019274: 1.83 TB (fastq) E-GEAD-872: 800 MB (expression matrix, HDF5) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
[DRA019233 / E-GEAD-867] microscopic polyangiitis (ICD10: M31.7): 6 cases (4 cases are also used in E-GEAD-635) 7 healthy donors (5 are also used in E-GEAD-635, 2 are also used in DRA019274 / E-GEAD-872) [DRA019274 / E-GEAD-872] SSc (ICD10: M34) with renal crisis: 1 case |
| Targets | BD Ab-seq |
| Target Loci for Capture Methods | Information on the antibodies used for antibody sequencing |
| Platform | Illumina [HiSeq 2500, NovaSeq 6000] |
| Library Source |
[DRA019233 / E-GEAD-867] RNAs extracted from a single cell isolated from white blood cells [DRA019274 / E-GEAD-872] RNAs extracted from a single cell isolated from whole blood leukocytes and kidney biopsy specimens |
| Cell Lines | - |
| Library Construction (kit name) | BD Rhapsody WTA Reagent Kit |
| Fragmentation Methods | Enzymatic Fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Software | BD Rhapsody Sequence Analysis Pipeline (version 1.12) |
| Reference Genome Sequence | GRCh38 |
| QC Methods | Cell Ranger Metrics |
| DDBJ Sequence Read Archive ID | |
| Genomic Expression Archive ID | |
| Total Data Volume |
DRA019233: 2 TB (fastq) E-GEAD-867: 10 GB (expression matrix, txt) DRA019274: 218 GB (fastq) E-GEAD-872: 800 MB (expression matrix, txt) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Takehisa Kitazawa
Affiliation: Research Division, Chugai Pharmaceutical Co., Ltd.
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Single-cell multi-omics analysis identifies two distinct phenotypes of newly-onset microscopic polyangiitis | doi: 10.1038/s41467-023-41328-0 | E-GEAD-635 |
| 2 | Neutrophil single-cell analysis identifies a uniquely primed subset and provides insights into predicting relapse of autoimmune small vessel vasculitis | E-GEAD-867 | |
| 3 | Single-cell analysis reveals immune cell abnormalities underlying the clinical heterogeneity of systemic sclerosis | DRA019274 E-GEAD-872 |
