NBDC Research ID: hum0272.v2

 

SUMMARY

Aims: Analysis of gene expression and somatic gene mutation in tumor cells and immune cells using skin tumor samples such as melanoma

Methods: whole exome sequencing analysis, RNA sequencing analysis, scRNA sequencing analyses, scTCR sequencing analyses

Participants/Materials: melanoma patients: 4 cases

 

Dataset IDType of DataCriteriaRelease Date
JGAS000285

NGS (Exome)

NGS (RNA-seq)

Controlled-access (Type I) 2021/12/20
JGAS000285 (Data addition)

NGS (Exome)

NGS (scRNA-seq)

NGS (scTCR-seq)

Controlled-access (Type I) 2022/02/07

*Release Note

*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

 

MOLECULAR DATA

Exome

Participants/Materials

melanoma (ICD10: C439): 4 cases

    cultured tumor cells established from melanoma patients: 4 cases, 4 + 1 samples

    lymph node metastatic lesions: 1 case, 2 samples

Targets Exome
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source DNAs extracted from cultured tumor cells and lymph nodes
Cell Lines -
Library Construction (kit name) Hybrid Selection
Fragmentation Methods Captured / Adaptor ligation
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 92 bp (mean)
Japanese Genotype-phenotype Archive Dataset ID JGAD000391
Total Data Volume 99.6 + 628.8 GB (bam [ref: hg38])
Comments (Policies) NBDC policy

 

RNA-seq

Participants/Materials

melanoma (ICD10: C439): 4 cases

    cultured tumor cells established from melanoma patients: 4 cases, 4 samples

Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source RNAs extracted from cultured tumor cells
Cell Lines -
Library Construction (kit name) Hybrid Selection
Fragmentation Methods Captured / Adaptor ligation
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp (mean)
Japanese Genotype-phenotype Archive Dataset ID JGAD000391
Total Data Volume 99.6 GB (fastq)
Comments (Policies) NBDC policy

 

scRNA-seq / scTCR-seq

Participants/Materials

melanoma (ICD10: C439): 3 cases

    tumor-infiltrating lymphocyte (TIL): 2 cases, 3 samples

    peripheral blood lymphocyte (PBL): 2 cases, 2 samples

    lymph node tumor-infiltrating lymphocyte (LN-TIL): 1 case, 2 samples

Targets scRNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source RNAs extracted from TIL, PBL and LN-TIL
Cell Lines -
Library Construction (kit name) Single Cell Immune Profiling Solution Kit
Fragmentation Methods Hybrid Selection
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp (mean)
Japanese Genotype-phenotype Archive Dataset ID JGAD000391
Total Data Volume 628.8 GB (fastq)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Takashi Inozume

Affiliation: Department of Dermatology, Chiba University

Project / Group Name: Development of more effective immunotherapy for skin cancer

Funds / Grants (Research Project Number):

NameTitleProject Number
KAKENHI Grant-in-Aid for Scientific Research (C) Identification of essential biomarkers for efficacy of anti-PD-1 therapy 19K08744

 

PUBLICATIONS

TitleDOIDataset ID
1 TIGIT/CD155 axis mediates resistance to immunotherapy in patients with melanoma with the inflamed tumor microenvironment doi: 10.1136/jitc-2021-003134 JGAD000391
2

 

USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use
Michiaki Hamada Faculty of Science and Engineering, Waseda University Japan Construction of RNA-targeted Drug Discovery Database JGAD000391 2022/12/26-2025/03/31