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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

JGAD000974

Type of data
NGS (WGS: PromethION)
NGS (WGS: Novaseq 6000)
Xenium In Situ Gene Expression
NGS (Visium Spatial Gene Expression), Histological image
NGS (snRNA-seq)
NGS (STOmics)
Spatial Proteomics
Access criteria
Controlled-access (Type I)
Total data volume
7.9 TB
File formats
  • FASTQ
  • BED
  • TSV
  • CSV
  • XLSX
  • JSON
  • MTX
  • HDF5
  • PNG
  • QPTIFF
  • TAR
Research
hum0455
Date published
2026-04-10
Date modified
2026-08-20
DDBJ Search
JGAD000974 (opens in a new tab)
JGA Study
JGAS000832 (opens in a new tab)

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
add-on_genes_list.pdfAdd-on custom panels104 KB
hum0455_MarkerList_79.pdf79 genes47.9 KB
hum0455_genelist_302.pdf302 genes153 KB

Analysis method

WGS

Materials and participants
pulmonary neuroendocrine carcinoma (ICD10: C34): 21 cases
frozen specimens
- tumor tissues: 21 samples
- non-tumor tissues: 21 samples
  • Health status
    Affected
  • Subject count
    21 (Individual)
Disease
  • pulmonary neuroendocrine carcinoma
Sample description
DNAs extracted from frozen specimen
  • Tissue
    Lung
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
Ligation Sequencing Kit (SQK-LSK114)
Fragmentation
N/A
Platform
Oxford Nanopore Technologies PromethION
Read type
Single-end
Read length
N/A
Reference genome
GRCh38
Mapping
Guppy (version 6.4.6 and 6.5.7), Minimap2 (version 2.24)
Mapping quality
N/A
Analysis method
Modkit (version 0.3.1)
Coverage (depth)
N/A
Coverage (breadth)
N/A
Data use policy
NBDC data sharing policy (JGAP000001)

WGS

Materials and participants
pulmonary neuroendocrine carcinoma (ICD10: C34): 1 case
frozen specimens
- tumor tissues: 1 sample
- non-tumor tissues: 1 sample
  • Health status
    Affected
  • Subject count
    1 (Individual)
Disease
  • pulmonary neuroendocrine carcinoma
Sample description
DNAs extracted from frozen specimen
  • Tissue
    Lung
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
TruSeq Nano DNA Library Prep 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 In Situ Gene Expression

Materials and participants
pulmonary neuroendocrine carcinoma (ICD10: C34): 33 cases
FFPE specimen
- tumor tissue: 36 samples
  • Health status
    Affected
  • Subject count
    33 (Individual)
Disease
  • pulmonary neuroendocrine carcinoma
Sample description
FFPE specimen
  • Tissue
    Lung
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
Spatial transcriptomics
Target
302 genes (Human Lung panel: 202 genes, custom: 100 genes)
Reagent kit
Xenium Decoding Consumables
Xenium Decoding Reagents
Xenium Slides & Sample Prep Reagents
Platform
10x Genomics Xenium Analyzer
Analysis method
xenium-1.3.0.6, xenium-1.4.0.7, xenium-1.7.1.0, xenium-2.0.0.10
Data use policy
NBDC data sharing policy (JGAP000001)

Visium Spatial Gene Expression, Histological image

Materials and participants
pulmonary neuroendocrine carcinoma (ICD10: C34): 19 cases
- tumor tissues: 19 samples
  • Health status
    Affected
  • Subject count
    19 (Individual)
Disease
  • pulmonary neuroendocrine carcinoma
Sample description
RNAs extracted from tumor tissues
  • Tissue
    Lung
  • 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
N/A
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
118 bp
Reference genome
GRCh38
Analysis method
spaceranger-1.3.1
Data use policy
NBDC data sharing policy (JGAP000001)

snRNA-seq

Materials and participants
pulmonary neuroendocrine carcinoma (ICD10: C34): 6 cases
- tumor tissues: 6 samples
  • Health status
    Affected
  • Subject count
    6 (Individual)
Disease
  • pulmonary neuroendocrine carcinoma
Sample description
RNAs extracted from tumor tissues
  • Tissue
    Lung
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
snRNA-seq
Target
N/A
Reagent kit
Chromium Nuclei Isolation Kit
Chromium GEM-X Single Cell 3' v4
Fragmentation
included in the above library construction kit
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
118 bp
Data use policy
NBDC data sharing policy (JGAP000001)

STOmics

Materials and participants
pulmonary neuroendocrine carcinoma (ICD10: C34): 2 cases
- tumor tissues: 2 samples
  • Health status
    Affected
  • Subject count
    2 (Individual)
Disease
  • pulmonary neuroendocrine carcinoma
Sample description
RNAs extracted from tumor tissues
  • Tissue
    Lung
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
Spatial transcriptomics
Target
N/A
Reagent kit
Stereo-Seq Transcriptomics Set
Fragmentation
included in the above library construction kit
Platform
MGI DNBSEQ-T7
Read type
Paired-end
Read length
135 bp
Data use policy
NBDC data sharing policy (JGAP000001)

Xenium In Situ Gene Expression

Materials and participants
pulmonary neuroendocrine carcinoma (ICD10: C34): 13 cases
FFPE specimen
- tumor tissue: 13 samples
  • Health status
    Affected
  • Subject count
    13 (Individual)
Disease
  • pulmonary neuroendocrine carcinoma
Sample description
FFPE specimen
  • Tissue
    Lung
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
Spatial transcriptomics
Target
5099genes
Xenium Prime 5K Human Pan Tissue & Pathways Panel : 5001 genes, Add-on custom panels：98genes
Reagent kit
Xenium Decoding Consumables
Xenium Decoding Reagents
Xenium Slides & Sample Prep Reagents
Platform
10x Genomics Xenium Analyzer
Analysis method
xenium-4.0.1.0
Data use policy
NBDC data sharing policy (JGAP000001)

Spatial Proteomics

Materials and participants
pulmonary neuroendocrine carcinoma (ICD10: C34): 13 cases
FFPE specimen
- tumor tissue: 13 samples
  • Health status
    Affected
  • Subject count
    13 (Individual)
Disease
  • pulmonary neuroendocrine carcinoma
Sample description
FFPE specimen
  • Tissue
    Lung
  • Tumor / normal
    Tumor
Sample provider
N/A
Experimental method
Spatial proteomics
Target
79 genes
Reagent kit
Staining Kit for PhenoCycler
Platform
Akoya Biosciences PhenoCycler
Analysis method
PhenoCycler-Fusion Acquisition Software
Data use policy
NBDC data sharing policy (JGAP000001)