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Dataset ID

JGAD000375

Type of data
NGS (Exome, Target Capture, RNA-seq)
Access criteria
Controlled-access (Type I)
Total data volume
545 GB
File formats
  • FASTQ
Research
hum0195
Date published
2022-03-04
Date modified
2025-12-08
DDBJ Search
JGAD000375 (opens in a new tab)
JGA Study
JGAS000269 (opens in a new tab)

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
Probe-Sequences.xlsx98 genes689 KB

Analysis method

WES

Materials and participants
liver cirrhosis and hepatocellular carcinoma after hepatitis C virus eradication (ICD10: K746, C220): 12 cases
tumor tissues: 12 samples
lymphocytes isolated from peripheral blood: 12 samples
chronic gastritis with gastric cancer (ICD10: C169): 11 cases
tumor tissues: 11 samples, non-tumor tissues: 38 samples, peripheral blood: 11 samples
gastric cancer (ICD10: C169): 1 + 1 case
tumor tissues: 2 samples
non-tumor tissues: 2 + 3 samples & peripheral blood: 1 + 1 sample
gastric submucosal tumor (ICD10: D371): 3 cases
non-tumor tissues: 6 samples, peripheral blood: 3 samples
  • Health status
    Affected
  • Subject count
    28 (Individual)
Disease
liver cirrhosis and hepatocellular carcinoma after hepatitis C virus eradication (K746, C220)
chronic gastritis with gastric cancer (C169)
gastric cancer (C169)
gastric submucosal tumor (D371)
Sample description
DNAs extracted from tumor tissues and lymphocytes isolated from peripheral blood of hepatocellular carcinoma
DNAs extracted from tumor tissues, non-tumor tissues, and peripheral blood samples of gastric cancer and gastric submucosal tumor
  • Tissue
    Lymphocyte, Peripheral blood
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
WES
Target
N/A
Reagent kit
Ion AmpliSeq Exome RDY Kit
Fragmentation
Enzymatic Fragmentation
Platform
Thermo Fisher Scientific Ion Proton
Read type
Single-end
Read length
150 bp
Data use policy
NBDC data sharing policy (JGAP000001)

RNA-seq

Materials and participants
liver cirrhosis and hepatocellular carcinoma after hepatitis C virus eradication (ICD10: K746, C220): 20 cases
non-tumor tissues: 20 samples
hepatitis C virus positive cirrhosis and hepatocellular carcinoma (ICD10: K746, C220): 3 cases
tumor tissues: 8 samples
non-tumor tissues: 3 samples
hepatitis C virus negative hepatocellular carcinoma (ICD10: C220): 2 cases
tumor tissues: 7 samples
non-tumor tissues: 2 samples
gastric cancer (ICD10: C169): 6 cases
intestinal metaplasia (IM) 5 samples, non-IM 3samples
  • Health status
    Affected
  • Subject count
    31 (Individual)
Disease
liver cirrhosis and hepatocellular carcinoma after hepatitis C virus eradication (K746, C220)
hepatitis C virus positive cirrhosis and hepatocellular carcinoma (K746, C220)
hepatitis C virus negative hepatocellular carcinoma (C220)
gastric cancer (C169)
Sample description
RNAs extracted from tumor tissues and non-tumor tissues of hepatocellular carcinoma
Total RNAs extracted from non-tumor tissues (only gland duct) of IM samples and non-IM samples
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
RNA-seq
Target
N/A
Reagent kit
TruSeq RNA Library Prep Kit
Fragmentation
Enzymatic Fragmentation
Platform
Illumina HiSeq 4000
Illumina NovaSeq 6000
Read type
Paired-end
Read length
101 bp
Data use policy
NBDC data sharing policy (JGAP000001)

Targeted DNA sequencing

Materials and participants
gastric cancer (ICD10: C169): 26 case (including 2 same cases in exome analysis)
non-tumor tissues: 96 samples
  • Health status
    Affected
  • Subject count
    26 (Individual)
Disease
gastric cancer (C169)
Sample description
DNAs extracted from non-tumor tissues of gastric cancer
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
Targeted DNA sequencing
Target
98 genes
Reagent kit
xGen Gene Capture Pools
Fragmentation
enzymatic fragmentation (enzymatic fragmentation kit Lotus (IDT)
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
150 bp
Data use policy
NBDC data sharing policy (JGAP000001)