NBDC Research ID: hum0286.v1
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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
Participants/Materials: Four samples (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.
URL: https://www.med.osaka-u.ac.jp/eng/activities/results/2022year/takehara2022-5-16
| Data Set ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000311 | NGS (Visium Spatial Gene Expression), Histological image | Controlled Access (Type I) | 2022/09/12 |
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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 Data set ID | JGAD000422 |
| Total Data Volume | 131.7 GB (fastq, tif, tsv) |
| 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 | Data Set 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 (Data Set ID) | Period of Data Use |
|---|---|---|---|---|---|
