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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

JGAD000745

Type of data
NGS (Visium Spatial Gene Expression), Histological image
Access criteria
Controlled-access (Type I)
Total data volume
65.8 GB
File formats
  • FASTQ
  • TSV
  • CSV
  • XLSX
  • JSON
  • MTX
  • CLOUPE
  • HTML
  • PNG
  • TIFF
Research
hum0399
Date published
2024-06-12
Date modified
2024-06-12
DDBJ Search
JGAD000745 (opens in a new tab)
JGA Study
JGAS000616 (opens in a new tab)

Analysis method

Visium spatial transcriptomics + histological image

Materials and participants
Breast cancer (ICD10: C509) patients harboring metastatic lymph nodes: 2 cases
non-metastatic lymph node: 2 samples
metastatic lymph node: 2 samples
  • Health status
    Affected
  • Subject count
    2 (Individual)
Disease
  • Breast cancer
Sample description
RNAs extracted from lymph nodes
  • Tissue
    Lymph node
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
Histological image
Spatial transcriptomics
Target
N/A
Sample processing
Histological staining: hematoxylin-eosin staining
Reagent kit
Visium CytAssist Spatial Gene Expression for FFPE
Fragmentation
Enzymatic fragmentation
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Reference genome
GRCh38
Analysis method
Space Ranger v2.0.0
Data use policy
NBDC data sharing policy (JGAP000001)