NBDC Research ID: hum0147.v1
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SUMMARY
Aims: Analysis of epigenetic status of regulatory T cells (Treg)
Methods: RNA-seq, ChIP-seq, PBAT-seq, ATAC-seq
Participants/Materials: Healthy donors
| Data Set ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000145 | Controlled Access (Type I) | 2020/05/25 |
* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data.
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 Data set 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 Data set 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 Data set 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 Data set ID | JGAD000214 |
| Total Data Volume | 1.6 TB (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 | 17gm0410016h0006 |
| 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 | 18gm0010005h0001 |
PUBLICATIONS
| Title | DOI | Data Set 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 |
USERS (Controlled-Access Data)
| Principal Investigator: | Affiliation: | Data in Use (Data Set ID) | Period of Data Use |
|---|---|---|---|
