NBDC Research ID: hum0268.v1
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SUMMARY
Aims: Proteogenomic discovery of a novel class of cancer antigens by HLA ligandome analysis of colon cancer tissues
Methods: RNA-seq, CAGE-seq and Iso-seq data were used to analyze the transcript variants coding an identified non-coding RNA-derived antigen.
Participants/Materials: Human colon cancer cell line: 1, colon cancer: 6
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000280 | NGS (Iso-seq, CAGE-seq, RNA-seq) | Controlled-access (Type I) | 2021/04/09 |
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MOLECULAR DATA
| Participants/Materials | Human colon cancer cell line (ICD10: C18): 1 sample |
| Targets | Iso-seq |
| Target Loci for Capture Methods | - |
| Platform | PacBio [Sequel] |
| Library Source | RNAs extracted from cells |
| Cell Lines | ATCC (CCL-220) |
| Library Construction (kit name) | SMRTbell Template Prep Kit 2.0 |
| Fragmentation Methods | SMRTbell Template Prep Kit 2.0 |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | - |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000386 |
| Total Data Volume | 16.1 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | Human colon cancer cell line (ICD10: C18): 1 sample |
| Targets | CAGE-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq] |
| Library Source | RNAs extracted from cells |
| Cell Lines | ATCC (CCL-220) |
| Library Construction (kit name) | - |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 75 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000386 |
| Total Data Volume | 16.1 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Human colon cancer cell line (ICD10: C18): 1 sample Colon cancer: 6 patients (6 tumor tissues and 5 non-tumor tissues) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from cells |
| Cell Lines | ATCC (CCL-220) |
| Library Construction (kit name) | TruSeq Stranded mRNA LT Sample Prep Kit |
| Fragmentation Methods | TruSeq Stranded mRNA LT Sample Prep Kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000386 |
| Total Data Volume | 153.2 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Takayuki Kanaseki
Affiliation: Department of Pathology, Sapporo Medical University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Proteogenomic discovery of HLA presented tumor antigens that arise from non-coding RNAs | JP20cm0106352 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | |||
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000386 | 2022/12/26-2025/03/31 |
