NBDC Research ID: hum0414.v1
SUMMARY
Aims: To analyze genomic aberrations and gene expression changes such as mutations, deletions, amplifications, and hypermethylation in human lung cancer cells at the somatic cell level, and to contrast these with clinicopathological information to elucidate the molecular mechanisms and characteristics of lung cancer development and progression at the genetic level.
Methods: Human small airway epithelial cells (SAEC) were immortalized via the expression of hTERT, a CDK4 mutant, and cyclin D1. After up to 35 days of 2D culture, SAECs expressing KRAS G12V (Control-ER-KRAS-G12V) showed a limited but significant anchorage-independent growth. These individual clones were named replication stress-tolerant cells (RSTC-2, RSTC-5, and RSTC-7). In this study, whole genome sequencing was performed on these five cell lines.
Participants/Materials: SAEC and its derived cell lines
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| DRA016800 | NGS (WGS) | Unrestricted-access | 2023/07/25 |
*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include them in the acknowledgment. Learn more
MOLECULAR DATA
| Participants/Materials |
SAEC and its derived cell lines: 5 samples (SAEC, Control-ER-KRAS-G12V, RSTC-2, RSTC-5, RSTC-7) |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNA extracted from cell lines |
| Cell Lines | SAEC (Lonza, Cat# CC-2547) |
| Library Construction (kit name) | TruSeq DNA PCR-Free Library Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| DDBJ Sequence Read Archive ID | DRA016800 |
| Total Data Volume | 900 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Bunsyo Shiotani
Affiliation: National Cancer Center Research Institute
Project / Group Name: Laboratory of Genome Stress Signaling
URL: https://www.ncc.go.jp/en/ri/division/genome_stress_signaling/index.html
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Fund for the Promotion of Joint International Research (Fostering Joint International Research (B)) | Elucidation of the mechanism underlying DNA replication stress response regulating genomic instability | 18KK0235 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Elucidation of the mechanism underlying tumor initiation via DNA replication stress regulated by ATR | 18H03378 |
| Core Research and Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST) | Development of an integrated cancer care system using artificial intelligence | JPMJCR1689 |
| AIP Challenge PRISM Acceleration Support Program (AIP-PRISM), Japan Science and Technology Agency (JST) | Development of the innovative drug discovery system using artificial intelligence | JPMJCR18Y4 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | An ATR-PrimPol pathway confers tolerance to oncogenic KRAS-induced and heterochromatin-associated replication stress. | doi: 10.1038/s41467-023-40578-2 | DRA016800 |
| 2 |
