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 IDType of DataCriteriaRelease Date
JGAS000145

NGS (RNA-seq)

NGS (ChIP-seq)

NGS (PBAT-seq)

NGS (ATAC-seq)

Controlled-access (Type I) 2020/05/25
JGAS000312

NGS (scRNA-seq)

NGS (bulk RNA-seq)

Controlled-access (Type I) 2022/02/18
JGAS000454 NGS (bulk RNA-seq) Controlled-access (Type I) 2023/05/08

*Release Note

*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

 

MOLECULAR DATA

NGS (RNA-seq)

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

 

NGS (ChIP-seq)

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

 

NGS (PBAT-seq)

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

 

NGS (ATAC-seq)

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

 

NGS (scRNA-seq)

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

 

NGS (bulk RNA-seq)

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 DOIDataset 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 InvestigatorAffiliationCountry/RegionResearch TitleData 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