NBDC Research ID: hum0160.v1
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SUMMARY
Aims: To investigate genomic alterations of Japanese esophageal squamous cell carcinomas
Methods: DNAs were extracted from esophageal squamous cell carcinoma tissues and paired non-cancer (normal) tissues. NGS libaraies were prepared by using TruSeq Nano DNA Low Throughput Library Prep Kit for whole genome sequencing (WGS). Sequencing was perfomred by Illumina HiSeq 2000/2500/X Five.
Participants/Materials: DNAs extracted from cancer tissues and non-cancer tissues of Japanese esophageal squamous cell carcinoma patients.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000155 | NGS (WGS) | Controlled-access (Type I) | 2019/05/28 |
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MOLECULAR DATA
| Participants/Materials |
esophageal squamous cell carcinoma (ICD10: C15): 20 cases cancer tissues: 20 samples paired non-cancer tissues: 20 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500/X Five] |
| Library Source | DNAs extracted from cancer tissues and paired non-cancer tissues from esophageal squamous cell carcinoma patients |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Nano DNA Low Throughput Library Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100-150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000233 |
| Total Data Volume | 3 TB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Hidewaki Nakagawa
Affiliation: RIKEN Center for Integrative Medical Sciences
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | - | ||
| 2 |
USERS (Controlled-Access Data)
| Principal Investigator | Affiliation | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|
| Kengo Kinoshita | Tohoku Medical Megabank Organization | Construction of Japanese whole genome database | JGAD000233 | 2019/06/24-2022/03/31 |
| Kouya Shiraishi | Division of Genome Biology, National Cancer Research Institute | Elucidation of immune-system networks between host and tumor based on genomic analysis | JGAD000233 | 2019/08/05-2023/03/31 |
