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 IDType of DataCriteriaRelease Date
JGAS000304 NGS (Exome) Controlled-access (Type I) 2022/07/07
JGAS000305 NGS (scRNA-seq) Controlled-access (Type I) 2022/07/07

*Release Note

*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

 

MOLECULAR DATA

JGAS000304

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

 

JGAS000305

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):

NameTitleProject Number
Grant-in-Aid for Scientific Research on Innovative Areas - Platforms for Advanced Technologies and Research Resources Platform for Advaced Genomic Science 16H06279

 

PUBLICATIONS

TitleDOIDataset 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 InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use