Skip to content
NBDC Human Database

No datasets in the cart.

Go to the cart

Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
We apologize for any inconvenience this may cause and appreciate your understanding.

We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

JGAD000946

Type of data
NGS (WGS, RNA-seq, EM-seq)
Xenium In Situ Gene Expression
Access criteria
Controlled-access (Type I)
Total data volume
196 GB
File formats
  • FASTQ
  • TAR
Research
hum0200
Date published
2026-02-05
Date modified
2026-02-05
DDBJ Search
JGAD000946 (opens in a new tab)
JGA Study
JGAS000804 (opens in a new tab)

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
gene_list.pdf379 genes188 KB

Analysis method

WGS

Materials and participants
IDC (ICD10: C509): 1 case
non-tumor tissue (normal breast tissue): 1 sample
  • Health status
    Affected
  • Subject count
    1 (Individual)
Disease
IDC (C509)
Sample description
DNAs extracted from tumor and non-tumor tissues
  • Tissue
    Breast
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
NEBNext Enzymatic Methyl-seq Kit
Fragmentation
Ultrasonic fragmentation (Covaris)
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
300 bp
Data use policy
NBDC data sharing policy (JGAP000001)

RNA-seq

Materials and participants
IDC (ICD10: C509): 1 case
non-tumor tissue (normal breast tissue): 1 sample
  • Health status
    Affected
  • Subject count
    1 (Individual)
Disease
IDC (C509)
Sample description
RNAs extracted from tumor and non-tumor tissues
  • Tissue
    Breast
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
RNA-seq
Target
N/A
Reagent kit
SMART-Seq Stranded Kit
Fragmentation
Heat treatment with Shearing Master Mix
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
300 bp
Data use policy
NBDC data sharing policy (JGAP000001)

EM-seq

Materials and participants
IDC (ICD10: C509): 1 case
non-tumor tissue (normal breast tissue): 1 sample
  • Health status
    Affected
  • Subject count
    1 (Individual)
Disease
IDC (C509)
Sample description
DNAs extracted from tumor and non-tumor tissues
  • Tissue
    Breast
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
EM-seq
Target
N/A
Reagent kit
NEBNext Enzymatic Methyl-seq Kit
Fragmentation
Ultrasonic fragmentation (Covaris)
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
300 bp
Data use policy
NBDC data sharing policy (JGAP000001)

Xenium 空間トランスクリプトーム

Materials and participants
IDC (ICD10: C509): 1 case
tumor tissue: 3 samples (primary tumor, metastatic lympho node, tumor-draining lymph node)
  • Health status
    Affected
  • Subject count
    1 (Individual)
Disease
IDC (C509)
Sample description
FFPE tumor tissues
  • Tissue
    Breast, Lymph node
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
Spatial transcriptomics
Target
379 genes (Human Breast panel: 280 genes, custom: 99 genes)
Platform
10x Genomics Xenium Analyzer
Analysis method
xenium-1.7.1.0
Data use policy
NBDC data sharing policy (JGAP000001)