Research ID
hum0350-v1Release info
Latest
Research title
Research to establish a foundation for integrated analysis of human genetic polymorphisms and omics data
Research overview
- Aims
- Among multifactorial diseases, there are many diseases involving the immune system (e.g., autoimmune diseases, allergic diseases, infectious diseases, cancer, and transplantation) for which there are few appropriate treatments. In order to solve these problems and find better treatments, we believe that a thorough understanding of human immune functions and an appropriate understanding of pathological conditions in these diseases are necessary. Therefore, this study aims to establish a new methodology for disease research based on omics analyses and genetic polymorphism analysis of immune cells such as lymphocytes derived from healthy individuals, and to accumulate important information for understanding pathological conditions and determining targets for drug discovery.
- Methods
- 5' and 3' single-cell RNA-seq, Micro-C and Region Capture Micro-C, CITE-seq and 5' single-cell RNA-seq, Multimodal assay including single-nucleus ATAC-seq, 3' and 5' single-nucleus RNA-seq, and 5' single-cell RNA-seq, MAS-seq, CAGE-seq, and NET-CAGE-seq were performed on CD4 positive T cells isolated from whole blood of three healthy Japanese. CAGE-seq was performed on CRISPR-activated Jurkat cells.
- Participants/materials
- Three healthy Japanese (one male, two females), CRISPR-activated Jurkat cells
- URL
- N/A
Datasets
| Cart | Dataset ID | Type of data | Analysis method | Access criteria | Date published |
|---|---|---|---|---|---|
| JGAD000822 | NGS (Micro-C and Region Capture Micro-C) NGS (CITE-seq and 5' single-cell RNA-seq) NGS (5' and 3' single-cell RNA-seq) NGS (Multimodal assay including single-nucleus ATAC-seq, 3' and 5' single-nucleus RNA-seq, and 5' single-cell RNA-seq) NGS (MAS-seq) NGS (CAGE-seq and NET-CAGE-seq) |
| Controlled-access (Type I) | 2024-06-14 | |
| E-GEAD-741 | NGS (Micro-C and Region Capture Micro-C) NGS (CITE-seq and 5' single-cell RNA-seq) NGS (5' and 3' single-cell RNA-seq) NGS (Multimodal assay including single-nucleus ATAC-seq, 3' and 5' single-nucleus RNA-seq, and 5' single-cell RNA-seq) NGS (MAS-seq) NGS (CAGE-seq and NET-CAGE-seq) |
| Unrestricted-access | 2024-05-14 | |
| E-GEAD-742 | NGS (Micro-C and Region Capture Micro-C) NGS (CITE-seq and 5' single-cell RNA-seq) NGS (5' and 3' single-cell RNA-seq) NGS (Multimodal assay including single-nucleus ATAC-seq, 3' and 5' single-nucleus RNA-seq, and 5' single-cell RNA-seq) NGS (MAS-seq) NGS (CAGE-seq and NET-CAGE-seq) |
| Unrestricted-access | 2024-05-14 | |
| E-GEAD-743 | NGS (Micro-C and Region Capture Micro-C) NGS (CITE-seq and 5' single-cell RNA-seq) NGS (5' and 3' single-cell RNA-seq) NGS (Multimodal assay including single-nucleus ATAC-seq, 3' and 5' single-nucleus RNA-seq, and 5' single-cell RNA-seq) NGS (MAS-seq) NGS (CAGE-seq and NET-CAGE-seq) |
| Unrestricted-access | 2024-05-14 | |
| E-GEAD-744 | NGS (Micro-C and Region Capture Micro-C) NGS (CITE-seq and 5' single-cell RNA-seq) NGS (5' and 3' single-cell RNA-seq) NGS (Multimodal assay including single-nucleus ATAC-seq, 3' and 5' single-nucleus RNA-seq, and 5' single-cell RNA-seq) NGS (MAS-seq) NGS (CAGE-seq and NET-CAGE-seq) |
| Unrestricted-access | 2024-05-14 | |
| E-GEAD-746 | NGS (Micro-C and Region Capture Micro-C) NGS (CITE-seq and 5' single-cell RNA-seq) NGS (5' and 3' single-cell RNA-seq) NGS (Multimodal assay including single-nucleus ATAC-seq, 3' and 5' single-nucleus RNA-seq, and 5' single-cell RNA-seq) NGS (MAS-seq) NGS (CAGE-seq and NET-CAGE-seq) |
| Unrestricted-access | 2024-05-14 | |
| E-GEAD-745 | NGS (Micro-C and Region Capture Micro-C) NGS (CITE-seq and 5' single-cell RNA-seq) NGS (5' and 3' single-cell RNA-seq) NGS (Multimodal assay including single-nucleus ATAC-seq, 3' and 5' single-nucleus RNA-seq, and 5' single-cell RNA-seq) NGS (MAS-seq) NGS (CAGE-seq and NET-CAGE-seq) |
| Unrestricted-access | 2024-05-14 | |
| E-GEAD-740 | NGS (Micro-C and Region Capture Micro-C) NGS (CITE-seq and 5' single-cell RNA-seq) NGS (5' and 3' single-cell RNA-seq) NGS (Multimodal assay including single-nucleus ATAC-seq, 3' and 5' single-nucleus RNA-seq, and 5' single-cell RNA-seq) NGS (MAS-seq) NGS (CAGE-seq and NET-CAGE-seq) |
| Unrestricted-access | 2024-05-14 | |
| DRA018405 | NGS (CAGE-seq [CRISPR-activated Jurkat cells]) |
| Unrestricted-access | 2024-04-30 | |
| E-GEAD-739 | NGS (CAGE-seq [CRISPR-activated Jurkat cells]) |
| Unrestricted-access | 2024-05-14 |
Data provider
- Principal investigator
- Kazuhiko Yamamoto
- Affiliation
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences
Research projects
No research projects.
Grants
| Name | Title | Project number |
|---|---|---|
KAKENHI Grant-in-Aid for Scientific Research (S) | Establishment of a novel strategy for pathological analysis of multifactorial diseases using genetic risk variants |
|
Japan Initiative for World-leading Vaccine Research and Development Centers, Japan Agency for Medical Research and Development (AMED) | Support institute for vaccine development by functional evaluation of human immune system through integration of genetic variations and multi-omics data |
|
Related publications
| Title | DOI | Dataset ID |
|---|---|---|
An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases |
Controlled access users
No use of the controlled access data has been recorded.