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 IDType of DataCriteriaRelease 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

*Release Note

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

 

MOLECULAR DATA

Exome

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

 

RNA-seq

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):

NameTitleProject Number
KAKENHI Grant-in-Aid for Scientific Research (B) Role of regeneration nodule in cirrhotic liver on tumorigenesis 17H04158

 

PUBLICATIONS

TitleDOIDataset 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 InvestigatorAffiliationCountry/RegionResearch TitleData 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