NBDC Research ID: hum0111.v1

 

SUMMARY

Aims: Genomic analysis of tumor infiltrating lymphocytes in gastric cancer

Methods: RNA-seq by Illumina HiSeq 2000 and amplicon sequencing of T/B cell antigen receptors by Illumina MiSeq

Participants/Materials: Specimens of 30 diffuse-type gastric carcinoma (matched tumor and normal tissue)

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000103

NGS (RNA-seq)

NGS (Amplicon-seq)

Controlled Access (Type I) 2017/07/31

*Release Note 

* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more

 

MOLECULAR DATA

NGS (RNA-seq)

Participants/Materials

diffuse-type gastric carcinoma (ICD10: C16): 30 cases

(tumor tissues only)

Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2000]
Library Source RNAs extracted from cancer tissues from gastric carcinoma patients
Cell Lines -
Library Construction (kit name) TruSeq Stranded mRNA Sample Prep Kit
Fragmentation Methods -
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp x 2
Japanese Genotype-phenotype Archive Data set ID JGAD00000000105
Total Data Volume 5.1MB (FPKM [txt])
Comments (Policies) NBDC policy

 

NGS (Amplicon-seq)

Participants/Materials

diffuse-type gastric carcinoma (ICD10: C16): 30 cases

(matched tumor and normal tissues)

Targets Amplicon-seq
Target Loci for Capture Methods V region to C region of TCRα, TCRβ, IgVH and IgVκ/λ genes
Platform Illumina [Miseq]
Library Source RNAs extracted from cancer and normal tissues from gastric carcinoma patients
Cell Lines -
Library Construction (kit name) Amplicon
Fragmentation Methods -
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 300 bp x 2
Japanese Genotype-phenotype Archive Data set ID JGAD00000000104
Total Data Volume 64GB (fastq [480 files])
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Shumpei Ishikawa

Affiliation: Department of Genomic Pathology, Medical Research Institute, Tokyo Medical and Dental University

Project / Group Name: -

Funds / Grants (Research Project Number):

Name Title Project Number
KAKENHI Grant-in-Aid for Young Scientists (A) Immunogenetic Repertoire Analysis for Tumor-infiltrating Lymphocytes - toward the Understanding of Tumor Immunity - 26710009
Project for Cancer Research and Therapeutic Evolution (P-CREATE) Integrated genomics of cancer cells and immune cells in gastric cancer 15655817
Basic Science and Platform Technology Program for Innovative Biological Medicine Technology development for obtaining functional and cancer-specific single-domain antigen receptor complex. 14014019

 

PUBLICATIONS

TitleDOIData Set ID
1 Immunogenetic Profiling for Gastric Cancers Identifies Sulfated Glycosaminoglycans as Major and Functional B-cell Antigens among Human Malignancies doi: 10.1016/j.celrep.2017.07.016 JGAD00000000104-JGAD00000000105
2

 

USERS (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use