NBDC Research ID: hum0286.v2
SUMMARY
Aims: To elucidate the interaction between cancer cells and immune cells in the tumor immune microenvironment of non-viral hepatocellular carcinoma
Methods: Visium Spatial Gene Expression Assay, Target Capture Sequencing Analysis
Participants/Materials:
Visium Spatial Gene Expression Assay: Four samples containing a fat-containing hepatocellular carcinoma (HCC) tissue#1, a non-tumor tissue of fat-containing HCC tissue#2, a fat-containing HCC tissue#3, and a fat-not containing HCC tissue#4. #1 and #2 are tissues derived from the same patient.
Target Capture Sequencing Analysis: Tumor tissues and non-tumor tissues of 55 hepatocellular carcinoma patients
URL: https://www.med.osaka-u.ac.jp/eng/activities/results/2022year/takehara2022-5-16
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000311 | NGS (Visium Spatial Gene Expression), Histological image | Controlled-access (Type I) | 2022/09/12 |
| JGAS000523 | NGS (Target Capture) | Controlled-access (Type I) | 2022/11/15 |
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MOLECULAR DATA
| Participants/Materials |
hepatocellular carcinoma (ICD10: C220): 3 cases fat-containing HCC: 2 sample non-tumor tissue of fat-containing HCC: 1 sample fat-not containing HCC: 1 sample |
| Targets | Visium Spatial Gene Expression |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from sample tissues |
| Cell Lines | - |
| Library Construction (kit name) | Visium Spatial Gene Expression Reagent Kits (10X Genomics) |
| Fragmentation Methods | enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 118 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000422 |
| Total Data Volume | 131.7 GB (fastq, tif, tsv) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
hepatocellular carcinoma (ICD10: C220): 55 cases tumor tissue: 55 samples, non-tumor tissue: 55samples |
| Targets | Target Capture |
| Target Loci for Capture Methods | promoter region of TERT gene + exonic regions of 69 genes |
| Platform | Thermo Fisher Scientific [Ion Proton] |
| Library Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Ion AmpliSeq Library Kit Plus, Ion AmpliSeq Kit for Chef DL8 |
| Fragmentation Methods | PCR |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 220 bp |
| Mapping Methods | BWA |
| Mapping Quality | Qscore >=20 |
| Reference Genome Sequence | GRCh38 |
| Coverage (Depth) | tumor tissue: 2000, non-tumor tissue: 1000 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000642 |
| Total Data Volume | 109.4 GB (bam) |
| Comments (Policies) | NBDC policy |
This study was supported by “Genome Science”. “Genome Science” is a part of the “Support Programs for Three Fields in Life Sciences (cancer, genome and brain sciences)” established by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) under the Grant-in-Aid for Scientific Research on Innovative Areas.
DATA PROVIDER
Principal Investigator: Takahiro Kodama
Affiliation: Dept. Gastroenterology and Hepatology, Graduate School of Medicine, Osaka University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Platform for Advanced Genome Science | 16H06279 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Multiomics identifies the link between intratumor steatosis and the exhausted tumor immune microenvironment in hepatocellular carcinoma | doi: 10.1002/hep.32573 | JGAD000422 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
