NBDC Research ID: hum0278.v1
SUMMARY
Aims: Identification of heterogeneity of breast cancer stem cells using genomic and single cell analyses.
Methods: Whole exome sequence analysis by using breast cancer cells sorted into cancer stem cells and non-cancer stem cells. Single cell RNA sequence of sorted breast cancer stem cells exploiting C1 system.
Participants/Materials: Breast cancer: 5 cases (scRNA: 4 cases, 11 samples; exome: 5 cases, 12 samples)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000304 | NGS (Exome) | Controlled-access (Type I) | 2022/07/07 |
| JGAS000305 | NGS (scRNA-seq) | Controlled-access (Type I) | 2022/07/07 |
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MOLECULAR DATA
| Participants/Materials |
Breast cancer (ICD10: C509): 5 cases cancer stem cells and non-cancer stem cells: 12 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Hiseq 3000/NovaSeq 6000] |
| Library Source | DNAs extracted from breast cancer cells sorted into cancer stem cells and non-cancer stem cells |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect XT HS V5 (Agilent Technologies) |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
200bp (100PE): HiSeq 300bp (150PE): NovaSeq |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000415 |
| Total Data Volume | 198.7 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Breast cancer (ICD10: C509): 4 cases cancer stem cells: 11 samples (cancer stem cells) |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Hiseq3000] |
| Library Source | RNAs extracted from sorted breast cancer stem cells |
| Cell Lines | - |
| Library Construction (kit name) | Nextera XT DNA Sample Preparation Kit (Illumina) |
| Fragmentation Methods | Tagmentation (Nextera XT DNA Sample Preparation Kit) |
| Spot Type | Single-end/Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 50bp (50SR)/200bp (100PE) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000416 |
| Total Data Volume | 332.7 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Noriko Gotoh
Affiliation: Division of Cancer Cell Biology, Cancer Research Institute, Kanazawa University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Grant-in-Aid for Scientific Research on Innovative Areas - Platforms for Advanced Technologies and Research Resources | Platform for Advaced Genomic Science | 16H06279 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Addiction to the IGF2-ID1-IGF2 circuit for maintenance of the breast cancer stem-like cells. | doi: 10.1038/onc.2016.293 | - |
| 2 | Semaphorin signaling via MICAL3 induces symmetric cell division to expand breast cancer stem-like cells. | doi: 10.1073/pnas.1806851116 | - |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
