NBDC Research ID: hum0147.v3
SUMMARY
Aims: Analysis of epigenetic status of regulatory T cells (Treg) and analysis of immune cells in cancers and autoimmune diseases
Methods: RNA-seq, ChIP-seq, PBAT-seq, ATAC-seq, single cell RNA-seq, and bulk RNA-seq
Participants/Materials: Healthy donors and cancer patients
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000145 | Controlled-access (Type I) | 2020/05/25 | |
| JGAS000312 | Controlled-access (Type I) | 2022/02/18 | |
| JGAS000454 | NGS (bulk RNA-seq) | Controlled-access (Type I) | 2023/05/08 |
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MOLECULAR DATA
| Participants/Materials: | 2 healthy donors (STR1, STR5) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Thermo Fisher Scientific [Ion S5] |
| Library Source |
RNAs extracted from 5 fractions from peripheral blood cells of healthy donors - Fraction 1: naive Treg - Fraction 2: effector Treg - Fraction 3: Foxp3+ effector conventional T cells - Fraction 5: effector conventional T cells - Fraction 6: naive T cells |
| Cell Lines | - |
| Library Construction (kit name) | KAPA Library Preparation Kit |
| Fragmentation Methods | KAPA Frag |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp on average |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000214 |
| Total Data Volume | 1.6 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | 1 healthy donor (STR1) |
| Targets | ChIP-seq |
| Target Loci for Capture Methods | - |
| Platform | Thermo Fisher Scientific [Ion S5] |
| Library Source |
DNAs extracted from 5 fractions from peripheral blood cells of healthy donors, and immunoprecipitated with an anti-histone antibody (H3K27ac) - Fraction 1: naive Treg - Fraction 2: effector Treg - Fraction 3: Foxp3+ effector conventional T cells - Fraction 5: effector conventional T cells - Fraction 6: naive T cells |
| Cell Lines | - |
| Library Construction (kit name) | KAPA Library Preparation Kit |
| Fragmentation Methods | Branson model1250D |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp on average |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000214 |
| Total Data Volume | 1.6 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | 4 healthy donors (STR1, STR5, STR6, BDR1) |
| Targets | PBAT-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500/NovaSeq 6000] |
| Library Source |
DNAs extracted from 5 fractions from peripheral blood cells of healthy donors - Fraction 1: naive Treg - Fraction 2: effector Treg - Fraction 3: Foxp3+ effector conventional T cells - Fraction 5: effector conventional T cells - Fraction 6: naive T cells
|
| Cell Lines | - |
| Library Construction (kit name) | EZ DNAMethylation-Gold Kit ver.2.1.3, ACCEL-NGS METHYL-SEQ DNA LIBRARY KIT ver3.0 |
| Fragmentation Methods | ACCEL-NGS METHYL-SEQ DNA LIBRARY KIT ver3.0 |
| Spot Type | Paired-end and Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100bp, 150bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000214 |
| Total Data Volume | 1.6 TB (fastq, tab [ref: GRCh38]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | 2 healty donors (STR1, STR5) |
| Targets | ATAC-seq |
| Target Loci for Capture Methods | - |
| Platform | Thermo Fisher Scientific [Ion S5] |
| Library Source |
DNAs extracted from 5 fractions from peripheral blood cells of healthy donors - Fraction 1: naive Treg - Fraction 2: effector Treg - Fraction 3: Foxp3+ effector conventional T cells - Fraction 5: effector conventional T cells - Fraction 6: naive T cells |
| Cell Lines | - |
| Library Construction (kit name) | KAPA Library Preparation Kit |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp on average |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000214 |
| Total Data Volume | 1.6 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: |
1 healthy donor (STR5) 5 cancer patients Bladder cancer (ICD10: C67), Colon cancer (ICD10: C20), Kidney cancer (ICD10: C64), Lung cancer (ICD10: C34.3), Ovarian cancer (ICD10: C56) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 3000] |
| Library Source | RNAs extracted from T cells of peripheral blood mononuclear cells from a healthy donor and tumor-infiltrating T cells from cancer patients |
| Cell Lines | - |
| Library Construction (kit name) | BD Rhapsody Targeted mRNA kits |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000423 |
| Total Data Volume | 279.9 GB (fastq, csv) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: |
Kidney cancer (ICD10: C64): 2 cases T cells of peripheral blood mononuclear cells: 6 fractions each tumor-infiltrating T cells: 4 fractions each Lung cancer (ICD10: C34): 3 cases tumor-infiltrating T cells: 2 fractions each |
| Targets | bulk RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500/4000] |
| Library Source | RNAs extracted from T cell fractions of peripheral blood mononuclear cells and tumor-infiltrating T cell fractions |
| Cell Lines | - |
| Library Construction (kit name) | KAPA Hyper Prep Kit |
| Fragmentation Methods | KAPA Frag |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID |
Kidney cancer: JGAD000423 Lung cancer: JGAD000571 |
| Total Data Volume |
JGAD000423: 279.9 GB (fastq) JGAD000571: 7.6 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shimon Sakaguchi
Affiliation: Experimental Immunology, IFReC, Osaka University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (B) | Clarification of regulatory T cell-specific epigenome | 15H04744 |
| Grant-in-Aid for Specially Promoted Research | Study of the function and development of regulatory T cells | 16H06295 |
| Core Research and Evolutional Science and Technology, Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED-CREST) | Devising novel methods to control chronic inflammation via regulatory T cells | JP17gm0410016 |
| Leading Advanced Projects for medical innovation, Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED-LEAP) | Study of Immunoregulatory technology targeting regulatory T cells | JP18gm0010005 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Regulatory T Cell-Specific Epigenomic Region Variants Are a Key Determinant of Susceptibility to Common Autoimmune Diseases | doi: 10.1016/j.immuni.2020.04.006 | JGAD000214 |
| 2 | CCR8-targeted specific depletion of clonally expanded Treg cells in tumor tissues evokes potent tumor immunity with long-lasting memory | doi: 10.1073/pnas.2114282119 | JGAD000423 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000214 | 2022/12/26-2025/03/31 |
| Yuta Kochi | Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University | Japan | Genetic study of complex diseases through comprehensive analysis of functional genetic variations | JGAD000214 | 2023/04/10-2024/03/31 |
