NBDC Research ID: hum0138.v2
SUMMARY
Aims: To elucidate the oncogenic potential of regeneration nodules in cirrhotic liver.
Methods: whole exome sequencing and RNA sequencing
Participants/Materials: liver cirrhosis, hepatocellular carcinoma and healthy donor
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000134 | NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2020/07/31 |
| JGAS000134 (Data addition) | NGS (RNA-seq) | Controlled-access (Type I) | 2021/03/26 |
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MOLECULAR DATA
| Participants/Materials |
Liver cirrhosis (ICD10: K746): 1 case (10 samples) Hepatocellular carcinoma (ICD10: C220): 4 cases (4 samples) |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNAs extracted from tumor, non-tumor, and cirrhosis tissues |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon v5 |
| Fragmentation Methods | Ultrasonic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000203 |
| Total Data Volume | 152 GB (bam [ref: GRCh37], fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Liver cirrhosis (ICD10: K746): 9 cases (15 samples) 7 healthy donors Normal livers from healthy donors for living-donor liver transplantation |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 4000] |
| Library Source | RNAs extracted from non-tumor and cirrhosis tissues from liver cirrhosis patients and normal livers from healthy donors |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq RNA Sample Preparation v2 |
| Fragmentation Methods | Ultrasonic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000203 |
| Total Data Volume |
Liver cirrhosis: 152 GB (bam [ref: GRCh37], fastq) Healthy donor: 16.7 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Atsushi Takai
Affiliation: Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (B) | Role of regeneration nodule in cirrhotic liver on tumorigenesis | 17H04158 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Comprehensive analysis of genetic aberrations linked to tumorigenesis in regenerative nodules of liver cirrhosis. | doi: 10.1007/s00535-019-01555-z | JGAD000203 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Robert Tsai | Institute of Biosciences & Technology, Texas A&M Health Science Center | Genome-wide Discovery of new Plasma DNA Mehylation Makers for Tracking the Progression of NAFLD to NASH and HCC | JGAD000203 | 2020/11/06-2022/08/31 | |
| Jinyan Huang | School of Medicine, Zhejiang University | Comprehensive analysis of alternative splicing in malignant tumors | JGAD000203 | 2022/03/07-2024/01/01 | |
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000203 | 2022/12/26-2025/03/31 |
