NBDC Research ID: hum0252.v1

SUMMARY

Aims: Study for molecular characteristics of adult T-cell leukemia-lymphoma and HTLV-1-associated diseases

Methods: Target capture sequencing, RNA-seq, and single cell RNA-seq (scRNA-seq)

Participants/Materials: ATL 6 cases, HTLV-1 infected carrier 10 cases (infected cells and unifected cells), and 3 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

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MOLECULAR DATA


Participants/Materials	ATL (ICD10: C915): 6 cases infected cells: 19 samples, unifected cells: 7 samples HTLV-1 infected carriers: 10 cases (including post-ATL specimens for 2 cases) infected cells: 20 samples, unifected cells: 10 samples
Targets	Target Capture
Target Loci for Capture Methods	280 genes including 50 candidate genes for ATL
Platform	Illumina [HiSeq 3000]
Library Source	DNAs extracted from infected cells and unifected 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)	200 bp
Japanese Genotype-phenotype Archive Dataset ID	JGAD000412
Total Data Volume	585.8 GB (fastq)
Comments (Policies)	NBDC policy


Participants/Materials	ATL (ICD10: C915): 4 cases CD4+ T cells from infected cells: 6 samples, unifected 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


Participants/Materials	ATL (ICD10: C915): 1 case (2 points) CD4+ T cells of infected cells: 4 samples, uninfected cells: 2 samples
Targets	scRNA-seq
Target Loci for Capture Methods	-
Platform	Illumina [HiSeq 2500/3000]
Library Source	RNAs extracted from single CD4+ T cells with/without infection of ATL
Cell Lines	-
Library Construction (kit name)	Chromium Single Cell 3’ Library v2 kit
Fragmentation Methods	included in the above library construction kit (enzymatic fragmentation)
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	124 bp
Japanese Genotype-phenotype Archive Dataset ID	JGAD000412
Total Data Volume	585.8 GB (fastq)
Comments (Policies)	NBDC policy

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

	Title	DOI	Dataset ID
1
2

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