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

JGAD000845

Type of data
NGS (scRNA-seq)
NGS (Visium Spatial Gene Expression), Histological image
Access criteria
Controlled-access (Type I)
Total data volume
449 GB
File formats
  • FASTQ
  • TXT
  • TSV
  • CSV
  • JSON
  • MTX
  • PNG
  • QPTIFF
Research
hum0461
Date published
2024-05-30
Date modified
2024-11-26
DDBJ Search
JGAD000845 (opens in a new tab)
JGA Study
JGAS000712 (opens in a new tab)

Analysis method

scRNA-seq

Materials and participants
esophageal squamous cell carcinoma (ICD10: C153, C154, C155): 5 cases, 11 samples
pre-RT: 4 samples
during RT: 3 samples
just after-RT: 2 samples
after RT: 2 samples
  • Health status
    Affected
  • Subject count
    11 (Sample)
Disease
esophageal squamous cell carcinoma (C153, C154, C155)
Sample description
RNAs extracted from tumor tissues
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
scRNA-seq
Target
N/A
Reagent kit
Chromium Single Cell 3' v3
Chromium Single Cell 5' v1
Fragmentation
enzymatic fragmentation
Platform
Illumina HiSeq 3000
Illumina NovaSeq 6000
Read type
Paired-end
Read length
126 bp
116 bp
Data use policy
NBDC data sharing policy (JGAP000001)

Multiplex Fluorescence Immunostaining

Materials and participants
esophageal squamous cell carcinoma (ICD10: C153, C154, C155): 2 cases, 2 samples
resected tissue from a patient who underwent surgery only (non-RT)
resected tissue from a patient who received preoperative RT
  • Health status
    Affected
  • Subject count
    2 (Individual)
Disease
esophageal squamous cell carcinoma (C153, C154, C155)
Sample description
surgically resected tissues
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
Multiplex fluorescence immunostaining
Target
N/A
Sample processing
Cell treatment: CODEX Staining Kit
Platform
Akoya Biosciences PhenoCycler
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)

Visium 空間トランスクリプトーム + 病理画像

Materials and participants
esophageal squamous cell carcinoma (ICD10: C153, C154, C155): 2 cases, 2 samples
resected tissue from a patient who underwent surgery only (non-RT)
resected tissue from a patient who received preoperative RT
  • Health status
    Affected
  • Subject count
    2 (Individual)
Disease
esophageal squamous cell carcinoma (C153, C154, C155)
Sample description
FFPE tumor samples from surgically resected tissues
  • Tissue
    Esophagus
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
Histological image
Spatial transcriptomics
Target
N/A
Sample processing
Histological staining: hematoxylin-eosin staining
Reagent kit
Visium Spatial Gene Expression
Fragmentation
enzymatic fragmentation
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
78 bp
Reference genome
GRCh38
Analysis method
spaceranger-1.3.1
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)