NBDC Research ID: hum0252.v3
SUMMARY
Aims: Study for molecular characteristics of adult T-cell leukemia-lymphoma and HTLV-1-associated diseases
Methods: Target capture sequencing, RNA-seq, single cell RNA-seq (scRNA-seq), Whole genome sequencing (WGS), scATAC-seq, ChIP-seq
Participants/Materials: ATL 6 + 4 + 6 cases, HTLV-1 infected carrier 10 cases (infected cells and unifected cells), and 3 + 1 healthy donors
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000301 | NGS (Target Capture, RNA-seq, scRNA-seq) | Controlled-access (Type I) | 2021/07/12 |
| JGAS000553 | NGS（Target Capture, WGS, scRNA-seq, scATAC-seq, ChIP-seq） | Controlled-access (Type I) | 2023/12/06 |
| JGAS000553 (Data addition) | NGS（Target Capture, scRNA-seq, scATAC-seq, ChIP-seq） | Controlled-access (Type I) | 2024/03/04 |
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MOLECULAR DATA
Target Capture (JGAS000301/JGAS000553)
| Participants/Materials |
[JGAS000301/JGAD000412] ATL (ICD10: C915): 6 cases infected cells: 19 samples, uninfected cells: 7 samples HTLV-1 infected carriers: 10 cases (including post-ATL specimens for 2 cases) infected cells: 20 samples, uninfected cells: 10 samples [JGAS000553/JGAD000674] ATL (ICD10: C915): 4 + 6 cases (total 30 + 23 samples) non-tumor cells: 4 + 11 samples tumor cells: before valemetostat treatment: 4 + 6 samples, after valemetostat treatment: 22 + 6 samples |
| Targets | Target Capture |
| Target Loci for Capture Methods | 280 genes including 50 candidate genes for ATL |
| Platform | Illumina [HiSeq 2500/3000, NovaSeq 6000] |
| Library Source | DNAs extracted from infected cells, uninfected cells, non-tumor and tumor cells of ATL and HTLV-1 carriers |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Target Enrichment System |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
JGAD000412, JGAD000674: 200 bp JGAD000674 (Data addition): 200 bp |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume |
JGAD000412: 585.8 GB (fastq) JGAD000674: 3.7 + 1.5 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
ATL (ICD10: C915): 3 cases (total 9 samples) non-tumor cells: 3 samples tumor cells: before valemetostat treatment: 3 samples, after valemetostat treatment: 3 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | MGI [DNBSEQ-G400] |
| Library Source | DNAs extracted from normal cells and tumor cells |
| Cell Lines | - |
| Library Construction (kit name) | MGIEasy PCR-Free DNA Library Prep Set |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 300 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000674 |
| Total Data Volume | 3.7 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
ATL (ICD10: C915): 4 cases CD4+ T cells from infected cells: 6 samples, uninfected cells: 2 samples CD4+ T cells from 3 cell lines |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from with/ without infected CD4+ T cells of ATL and CD4+ T cells of healthy donors |
| Cell Lines | Human Peripheral Blood CD4+ T cells (Lonza Catalog #: 2W-200) |
| Library Construction (kit name) | NEBNext UltraTM RNA Library Prep Kit for Illumina |
| Fragmentation Methods | included in the above library construction kit (chemical reaction [Mg2+, heat treatment]) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 300 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000412 |
| Total Data Volume | 585.8 GB (fastq) |
| Comments (Policies) | NBDC policy |
scRNA-seq (JGAS000301/JGAS000553)
| Participants/Materials |
[JGAS000301/JGAD000412] ATL (ICD10: C915): 1 case (2 points) CD4+ T cells of infected cells: 4 samples, uninfected cells: 2 samples [JGAS000553/JGAD000674] ATL (ICD10: C915): 3 + 3 cases (total 10 + 11 samples) peripheral blood lymphocytes: before valemetostat treatment: 3 + 7 samples, after valemetostat treatment: 7 + 4 samples |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500/3000, NovaSeq 6000] |
| Library Source | RNAs extracted from single CD4+ T cells with/without infection of ATL or peripheral blood lymphocytes of ATL cases before and after valemetostat treatment |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Single Cell 3’ Reagent Kits v2, Chromium Single Cell 5′ Reagent Kits |
| Fragmentation Methods | included in the above library construction kit (enzymatic fragmentation) |
| Spot Type |
JGAD000412, JGAD000674: Paired-end JGAD000674 (Data addition): Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
JGAD000412, JGAD000674: 124 bp JGAD000674 (Data addition): 91-98 bp |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume |
JGAD000412: 585.8 GB (fastq) JGAD000674: 3.7 + 1.5 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
ATL (ICD10: C915): 3 + 3 cases (total 10 + 11 samples) peripheral blood lymphocytes: before valemetostat treatment: 3 + 7 samples, after valemetostat treatment: 7 + 4 samples |
| Targets | scATAC-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from peripheral blood lymphocytes of ATL cases before and after valemetostat treatment |
| Cell Lines | - |
| Library Construction (kit name) | Chromium NextGEM Single Cell ATAC Reagent Kits v1.1 |
| Fragmentation Methods | enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
JGAD000674: 100 bp JGAD000674 (Data addition): 50× 49 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000674 |
| Total Data Volume | 3.7 + 1.5 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
ATL (ICD10: C915): 1 + 2 case CD4+ T cells from 1 cell line |
| Targets | ChIP-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq 500] |
| Library Source |
DNAs extracted from CD4+ T cells and tumor cells and immunoprecipitated with anti-histone antibodies (H3K27me3, H3K27ac) ATL tumor cells before valemetostat treatment: control 1 + 2 sample, ChIP 2 + 2 samples ATL tumor cells after valemetostat treatment: ChIP 2 + 4 samples CD4+ T cells: control 1 sample, ChIP 2 samples |
| Cell Lines | Human Peripheral Blood CD4+ T cells (Lonza Catalog #: 2W-200) |
| Library Construction (kit name) | Standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 75 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000674 |
| Total Data Volume | 3.7 + 1.5 TB（fastq） |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Makoto Yamagishi
Affiliation: Graduate School of Frontier Sciences, The University of Tokyo
Project / Group Name:
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Research Program on Emerging and Re-emerging Infectious Diseases, Japan Agency for Medical Research and Development (AMED) | Comprehensive study on elucidation of pathogenesis of HTLV-1 infection based on genome information and development of risk prediction algorithm | JP23fk0108672 |
| Research Program on Emerging and Re-emerging Infectious Diseases, Japan Agency for Medical Research and Development (AMED) | Development of risk stratification and prevention for HTLV-1-associated diseases based on multi-omics database | JP22fk0108126 |
| Japan Program for Infectious Diseases Research and Infrastructure, Japan Agency for Medical Research and Development (AMED) | Integrated data science for deciphering the epigenomic code and molecular network of HTLV-1 infection and strategic drug discovery | JP23wm0325056 |
| Japan Program for Infectious Diseases Research and Infrastructure, Japan Agency for Medical Research and Development (AMED) | Deep exploration for retrovirus reservoir heterogeneity and host-virus interaction by multi-phase single-cell epigenetic analysis | JP22wm0325017 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Genome-based medicine and clinical stratification for NOTCH1-mutated malignant lymphomas | JP22ck0106703 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | A nation-wide registry and biorepository system for patients with aggressive adult T-cell leukemia-lymphoma | JP23ck0106860 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Mechanisms of cooperative clonal evolution of ATL by genomic and epigenomic abnormalities | 21K08386 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Mechanisms of action and resistance in histone methylation-targeted therapy | doi: 10.1038/s41586-024-07103-x | JGAD000674 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Masao Matsuoka | Kumamoto University School of Medicine Hematology, Rheumatology and Infectious Diseases | Japan | Retrospective observational study of characteristics, clinical course and treatment of malignant lymphoma and adult T-cell leukemia/lymphoma with genetic and pathological evaluations | JGAD000412 | 2022/05/16-2030/03/31 |
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000412 | 2022/12/26-2025/03/31 |
