NBDC Research ID: hum0284.v1



Aims: To clarify expressional changes from precancerous to malignancy by single-cell RNA-seq analysis of breast cancer clinical specimens

Methods: Cells were isolated from the surgically resected tumor tissue. Single-cell sequence library was constructed using 10xChromium kit. Single-cell gene expression analysis was performed by a next-generation sequencer.

Participants/Materials: Primary tumor samples collected from breast cancer patients


Dataset IDType of DataCriteriaRelease Date
JGAS000309 NGS (scRNA-seq) Controlled-access (Type I) 2023/01/19

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breast invasive carcinoma (ICD10: C50): 4 cases

   surgically resected tumor tissue: 4 samples

Targets scRNA-seq
Target Loci for Capture Methods -
Platform Illumina [NovaSeq 6000]
Library Source RNAs extracted from isolated cells abteined from surgically resected tumor tissues.
Cell Lines -
Library Construction (kit name) Chromium Next GEM Single Cell 3' Reagent Kits v3.1
Fragmentation Methods Chromium Next GEM Single Cell 3' Reagent Kits v3.1
Spot Type Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) -
Japanese Genotype-phenotype Archive Dataset ID JGAD000420
Total Data Volume 134.5 GB (fastq)
Comments (Policies) NBDC policy



Principal Investigator: Jun Nakayama

Affiliation: Division of Cellular Signaling, National Cancer Center Research Institute

Project / Group Name: Laboratory of Integrative Oncology

Funds / Grants (Research Project Number):

NameTitleProject Number
KAKENHI Grant-in-Aid for JSPS Research Fellows Analysis of Cancer Evolution by Single Cell Amplicomics 20J01794



TitleDOIDataset ID
1 Single-Cell Transcriptome Profiling Reveals Intratumoral Heterogeneity and Molecular Features of Ductal Carcinoma In Situ doi: 10.1158/0008-5472.CAN-22-0090 JGAD000420


USRES (Controlled-access Data)

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