NBDC Research ID: hum0350.v1
SUMMARY
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
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
|
JGAS000689 E-GEAD-740 E-GEAD-741 E-GEAD-742 E-GEAD-743 E-GEAD-744 E-GEAD-745 E-GEAD-746 |
NGS (Micro-C and Region Capture Micro-C) NGS (CITE-seq and 5' single-cell RNA-seq) |
Controlled-access (Type I) Unrestricted-access |
2024/06/13 |
|
DRA018405 E-GEAD-739 |
NGS (CAGE-seq [CRISPR-activated Jurkat cells]) | Unrestricted-access | 2024/06/13 |
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MOLECULAR DATA
Micro-C and Region Capture Micro-C
| Participants/Materials | 3 healthy Japanese (17 samples) |
| Targets | Micro-C and Region Capture Micro-C |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | genomic DNA extracted from CD4 positive T cells isolated from whole blood |
| Cell Lines | - |
| Library Construction (kit name) | Dovetail Micro-C Kit |
| Fragmentation Methods | MNase |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 400 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000822 |
| Total Data Volume | 17.8 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | 3 healthy Japanese (20 samples) |
| Targets | 5' and 3' single-cell RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | polyA RNA extracted from CD4 positive T cells isolated from whole blood |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 5′ and 3′ kits |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 350 bp |
| Software | Cell Ranger version 5.0.1 |
| Reference Genome Sequence | GRCh38 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000822 |
| Genomic Expression Archive ID | E-GEAD-741 |
| Total Data Volume |
JGAD000822: 17.8 TB (fastq) E-GEAD-741: 4.6 GB (matrix) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | 3 healthy Japanese (9 samples) |
| Targets | Multimodal assay including single-nucleus ATAC-seq, 3' and 5’ single-nucleus RNA-seq, and 5' single-cell RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | polyA RNA and genomic DNA extracted from CD4 positive T cells isolated from whole blood |
| Cell Lines | - |
| Library Construction (kit name) |
(5′single-nucleus RNA-seq and 5′single-cell RNA-seq) Chromium Next GEM Single Cell 5′kit (single-nucleus ATAC-seq and 3′single-nucleus RNA-seq) Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 300 or 350 bp |
| Software | Cell Ranger version 5.0.1 |
| Reference Genome Sequence | GRCh38 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000822 |
| Genomic Expression Archive ID | |
| Total Data Volume |
JGAD000822: 17.8 TB (fastq) E-GEAD-742: 43 GB (tsv) E-GEAD-743: 6.8 GB (matrix) E-GEAD-744: 2.0 GB (bed, matrix) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | 2 healthy Japanese (6 samples) |
| Targets | CAGE-seq and NET-CAGE-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq 500] |
| Library Source | total RNA and nuclear RNA from CD4 positive T cells isolated from whole blood |
| Cell Lines | - |
| Library Construction (kit name) | CAGE Preparation Kit |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | - |
| Mapping Methods | STAR version 2.7.10b |
| Reference Genome Sequence | hg38 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000822 |
| Genomic Expression Archive ID | E-GEAD-746 |
| Total Data Volume |
JGAD000822: 17.8 TB (fastq) E-GEAD-746: 52 MB (bed) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | 1 healthy Japanese (2 samples) |
| Targets | MAS-seq |
| Target Loci for Capture Methods | - |
| Platform | PacBio [Sequel Ⅱ] |
| Library Source | polyA RNA extracted from CD4 positive T cells isolated from whole blood |
| Cell Lines | - |
| Library Construction (kit name) | MAS-Seq for 10x Single Cell 3’ kit with minor modifications against TSO PCR primers to adapt it to 5′ scRNA-seq cDNA |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | - |
| Software | CCS software version 6.3.0, SMRT Link version 12, Stringtie2 version 2.2.1 |
| Reference Genome Sequence | hg38 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000822 |
| Genomic Expression Archive ID | E-GEAD-745 |
| Total Data Volume |
JGAD000822: 17.8 TB (fastq) E-GEAD-745: 14 MB (GTF) |
| Comments (Policies) | NBDC policy |
CITE-seq and 5' single-cell RNA-seq
| Participants/Materials | 3 healthy Japanese (8 samples) |
| Targets | CITE-seq and 5' single-cell RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | Cell surface proteins and total RNA of CD4-positive T cells isolated from whole blood |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 5′ kits with Feature Barcode technology for Cell Surface Protein |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 73 bp |
| Software | Cell Ranger version 5.0.1 |
| Reference Genome Sequence | GRCh38 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000822 |
| Genomic Expression Archive ID | E-GEAD-740 |
| Total Data Volume |
JGAD000822: 17.8 TB (fastq) E-GEAD-740: 3.4 GB (bed, matrix) |
| Comments (Policies) | NBDC policy |
CAGE-seq (CRISPR-activated Jurkat cells)
| Participants/Materials | CRISPR-activated Jurkat cells: 15 samples |
| Targets | CAGE-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | Total RNA from CRISPR-activated Jurkat cells |
| Cell Lines | RIKEN BRC RCB0806 |
| Library Construction (kit name) | CAGE Preparation Kit |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | - |
| Mapping Methods | STAR version 2.7.10b |
| Reference Genome Sequence | hg38 |
| DDBJ Sequence Read Archive ID | DRA018405 |
| Genomic Expression Archive ID | E-GEAD-739 |
| Total Data Volume |
DRA018405: 292 GB (fastq) E-GEAD-739: 424 MB (bed) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Kazuhiko Yamamoto
Affiliation: Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences
Project / Group Name: -
Funds / Grants (Research Project Number):
| 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 | 18H05285 |
| 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 | JP223fa627010 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases. (Science 2024 in press) | JGAD000822 DRA018405 E-GEAD-739 E-GEAD-740 E-GEAD-741 E-GEAD-742 E-GEAD-743 E-GEAD-744 E-GEAD-745 E-GEAD-746 |
|
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
