NBDC Research ID: hum0394.v2
SUMMARY
Aims: We perform spatial transcriptome analysis and other omics analyses, such as genome/epigenome sequencing and multiplexed immunofluorescence, using fresh-frozen and FFPE specimens of non-small cell lung cancers. We try to develop a novel stratification method for lung cancer patients by considering intratumor heterogeneity and conditions of complicated microenvironments of cancer tissues. We aim to characterize omics statuses of cancer cells and their surrounding stromal cells and immune cells, such as cancer-associated fibroblasts and tumor-infiltrating lymphocytes, at a spatial level and evaluate tumor cell-microenvironment relationships at a molecular level.
Methods: Spatial transcriptome sequencing Visium, high-performance in situ gene expression mapping Xenium, Multiplex Fluorescence Immunostaining, Whole Genome Sequencing and Targeted Long-Read Methylation Sequencing (t-nanoEM)
Participants/Materials:
[Visium] 16 tumor sections from 8 non-small cell lung cancer patients
[Xenium] Five tumor sections from 5 non-small cell lung cancer patients
[WGS] 1 tumor section and 1 non-tumor section from 1 non-small cell lung cancer patient
[t-nanoEM] Five microdissected tumor regions from 1 non-small cell lung cancer patient
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000613 |
NGS (Visium Spatial Gene Expression), Histological image |
Controlled-access (Type I) | 2024/04/08 |
| JGAS000757 | NGS (WGS, t-nanoEM) | Controlled-access (Type I) | 2024/11/20 |
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MOLECULAR DATA
Visium Spatial Gene Expression, Histological image
| Participants/Materials |
non-small cell lung cancer (ICD10: C349): 8 cases surgical section: 16 samples |
| Targets | Visium Spatial Gene Expression |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from surgical sections (fresh-frozen/FFPE) |
| Cell Lines | - |
| Library Construction (kit name) | Visium Spatial Gene Expression Reagent Kits |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
fresh-frozen: 118 bp FFPE: 78 bp |
| Software | spaceranger-1.2.1, spaceranger-1.3.0 |
| QC | - |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000742 |
| Total Data Volume | 479.7 GB (fastq, png, json, csv, tsv, mtx, cloupe, html) |
| Comments (Policies) | NBDC policy |
Xenium In Situ Gene Expression
| Participants/Materials |
non-small cell lung cancer (ICD10: C349): 5 cases surgical section: 5 samples |
| Targets | Xenium In Situ Gene Expression |
| Target Loci for Capture Methods | 302 genes (Human Lung panel: 202 genes, custom: 100 genes） |
| Platform | 10x Genomics [Xenium Analyzer] |
| Source | surgical sections (fresh-frozen/FFPE) |
| Cell Lines | - |
| Reagents (Panel, Kit, Version) |
Xenium Slides & Sample Prep Reagents Xenium Decoding Reagents Xenium Decoding Consumables |
| Software | xenium-1.1.0.2, xenium-1.2.0.3 |
| QC | - |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000742 |
| Total Data Volume | 479.7 GB (csv, h5, html, json, mtx, tiff, parquet, tsv, xenium, zarr) |
| Comments (Policies) | NBDC policy |
Multiplex Fluorescence Immunostaining
| Participants/Materials |
lung adenocarcinoma (ICD10: C349): 3 cases tumor tissues: 3 samples |
| Targets | Multiplex Fluorescence Immunostaining |
| Target Loci for Capture Methods | cycle/probe information |
| Platform | Akoya Biosciences [PhenoCycler] |
| Library Source | tumor tissues of lung adenocarcinomas |
| Cell Lines | - |
| Cell Treatment Method (kit name) | Staining Kit for PhenoCycler |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000742 |
| Total Data Volume | 479.7 GB (qptiff) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
non-small cell lung cancer (ICD10: C349): 1 case tumor tissue: 1 sample (Illumina, Nanopore) non-tumor tissue: 1 sample (Illumina) |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform |
Illumina [NovaSeq 6000] Nanopore [PromethION] |
| Library Source | DNAs extracted from tumor tissue and non-tumor tissue |
| Cell Lines | - |
| Library Construction (kit name) |
Illumina: TruSeq Nano DNA Library Prep Kit, NEBNext Ultra II DNA Library Prep Kit and NEBNext Multiplex Oligos for Illumina Nanopore: Ligation Sequencing Kit V14 (SQK-LSK114) |
| Fragmentation Methods |
Illumina: Ultrasonic fragmentation (Covaris) Nanopore: - |
| Spot Type |
Illumina: Paired-end Nanopore: Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
Illumina: 300 bp Nanopore: 7,500 bp on average |
| Mapping Methods |
Illumina: BWA-MEM Nanopore: Guppy |
| Mapping Quality | - |
| Reference Genome Sequence | hg38 |
| Coverage (Depth) | Illumina: x44 (non-tumor tissue), x82 (tumor tissue) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000898 |
| Total Data Volume | 616.6 GB (fastq, bam) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
non-small cell lung cancer (ICD10: C349): 1 case five microdissected tumor regions: 1 sample |
| Targets | t-nanoEM |
| Target Loci for Capture Methods | Twist Alliance Pan-cancer Methylation Panel - 1.5 MB |
| Platform | Nanopore [PromethION] |
| Source | DNA extracted from tumor tissue sample |
| Cell Lines | - |
| Library Construction (kit name) |
NEBNext Enzymatic Methyl-seq Kit The five libraries were pooled and subjected to target enrichment using the Twist Standard Hyb and Wash Kit v2 with a pan-cancer panel. |
| Fragmentation Methods | Covaris g-TUBE |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 4,800 bp on average |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000898 |
| Total Data Volume | 616.6 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Ayako Suzuki
Affiliation: Laboratory of Medical Omics Data Analysis, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Early-Career Scientists | Development of spatial genome and transcriptome analytical methods in local regions of lung cancer tissues | 21K15566 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | |||
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
