NBDC Research ID: hum0477.v1
SUMMARY
Aims: Cancer is the leading cause of death in Japan and is continuing to rise. It has been reported that tumor microenvironment is linked to the tumor development, invasion, metastasis and residence of cancer to therapy. Organoid can reproduce its organ structure and function, there are expectations for their application in biomedical research, regenerative medicine, and human disease study. We collected tissues from patients with gastrointestinal tract or suspected tumors treated at Gunma University Hospital to avoid inconveniences in diagnosis and treatment. We perform organoid culture, analyzing their properties and mechanism related to cancer cells and microenvironment. This research is expected to identify mechanisms of tumor development, novel therapeutic targets and develop new therapies.
Methods: RNA-seq analysis of epithelial cells from human colon organoid and Caco-2 cells was conducted before and after co-cultivation of epithelial cells and Bifidobacterium longum subsp. longum (B. longum) for 24 hours.
Participants/Materials: Healthy tissues from a colorectal cancer patient (before/after co-cultivation with Bifidobacterium): 1 sample each
Caco-2 cells (before/after co-cultivation with Bifidobacterium): 1 sample each
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000740 | NGS (RNA-seq) | Controlled-access (Type I) | 2024/10/16 |
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MOLECULAR DATA
| Participants/Materials |
- Epithelial cells from healthy colon organoid from a colorectal cancer (ICD10: C18.6) patient before co-cultivation with B. longum: 1 sample after co-cultivation with B. longum: 1 sample - Caco-2 cells before co-cultivation with B. longum: 1 sample after co-cultivation with B. longum: 1 sample |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq 1000] |
| Library Source | RNAs extracted from epithelial cells or Caco-2 cells |
| Cell Lines | Caco-2 cells |
| Library Construction (kit name) | Illumina Stranded mRNA Prep, IDT for Illumina RNA UD Indexes Set A-B Ligation |
| Fragmentation Methods | Exposure to cations at high temperature conditions |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp x 2 |
| Software | HISAT2 |
| Reference Genome Sequence | GRCh38 |
| QC | FastQC |
| Gene Number | 60,606 genes |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000875 |
| Total Data Volume | 16.0 GB (fastq, csv) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Nobuo Sasaki
Affiliation: Laboratory of Mucosal Ecosystem Design, Institute for Molecular and Cellular Regulation, Gunma University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Project Focused on Developing Key Technology for Discovering and Manufacturing Drugs for Next-Generation Treatment and Diagnosis, Japan Agency for Medical Research and Developmstent (AMED) | Development of Scalable Platform of the Drug Discovery Targeting for Human Mucosal Ecosystem | JP23ae0121046 |
| Fusion Oriented REsearch for disruptive Science and Technology (FOREST) program, Japan Science and Technology Agency (JST) | Development of a novel culturing system for gut bacteria to regulate adult tissue stem cells | JPMJFR2161 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Generating the next generation of organoid biobank to reveal intestinal environment-dependent tumorigenesis | 23H02713 |
| KAKENHI Grant-in-Aid for Challenging Research (Pioneering) | Predictive modeling of bacteria variation using in vitro reconstructions of the human gut ecosystem | 23K17415 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | |||
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|
