NBDC Research ID: hum0120.v2

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SUMMARY

Aims: To identify the biomarkers of predicting metastasis and reccurence in colorectal cancer (CRC).

Methods: DNAs and RNAs were extracted from tumor and matched normal tissues. Whole exome sequencing were performed uisng tumor and matched normal tissues. RNA-seq and TCR repertoire analysis were performed using tumor tissues.

Participants/Materials: 10 cases of stage 1 and 2 CRCs, which cases occurred liver or lung metastasis.

 

Dataset IDType of DataCriteriaRelease Date
JGAS000221 NGS (Exome) Controlled-access (Type I) 2020/04/03
DRA011183 NGS (Exome) Unrestricted-access 2020/04/03
DRA011184 NGS (RNA-seq) Unrestricted-access 2020/04/03
DRA011185 NGS (Target Capture) Unrestricted-access 2020/10/30

*Release Note

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

*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more

 

MOLECULAR DATA

Exome

Participants/Materials

CRC (ICD10: C189): 10 cases (36 samples)

   - tumor tissues (colon: 10 samples, liver: 9 samples, lung: 5 samples)

   - non-tumor mucosa tissues (colon: 8 samples, lung: 4 samples)

Targets Exome
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source DNAs extracted from tumor and matched non-tumor tissues from CRCs
Cell Lines -
Library Construction (kit name) SureSelect Human ALL Exon V5
Fragmentation Methods Ultrasonic fragmentation (Covaris)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp
Japanese Genotype-phenotype Archive Dataset ID / DDBJ Sequence Read Archive ID

non-tumor tissues: JGAD000311

tumor tissues: DRA011183

Total Data Volume 414 GB (fastq)
Comments (Policies) NBDC policy

 

RNA-seq

Participants/Materials

CRC (ICD10: C189): 10 cases (20 samples)

   - primary tumor tissues: 8 samples

   - metastatic tumor tissues: 12 samples

Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source RNAs extracted from tumor tissues from CRC
Cell Lines -
Library Construction (kit name) Agilent SureSelect Strand Specific RNA Kit
Fragmentation Methods Heat treatment
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp
DDBJ Sequence Read Archive ID DRA011184
Total Data Volume 414 GB (fastq)
Comments (Policies) NBDC policy

 

Target Capture

Participants/Materials

CRC (ICD10: C189): 10 cases (20 samples)

   - primary tumor tissues: 8 samples

   - metastatic tumor tissues: 12 samples

Targets Target Capture
Target Loci for Capture Methods T-cell receptor β chain region
Platform Illumina [HiSeq 2500]
Library Source RNAs extracted from tumor tissues from CRC
Cell Lines -
Library Construction (kit name) KAPA HiFi HotStart Ready Mix PCR Kit
Fragmentation Methods Heat treatment
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp
DDBJ Sequence Read Archive ID DRA011185
Total Data Volume 16 GB (fastq)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Koshi Mimori

Affiliation: Department of Surgery, Kyushu University Beppu Hospital

Project / Group Name: -

URL: https://www.beppu.kyushu-u.ac.jp/gekareview/en/

Funds / Grants (Research Project Number):

NameTitleProject Number
Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) Understanding of molecular mechanisms to generate genetic heterogeneity associated with micro-environmental diversity for development of novel therapy and diagnostic technology in intractable cancers. JP19cm0106504

 

PUBLICATIONS

TitleDOIDataset ID
1
2

 

USRES (Controlled-access Data)

Principal InvestigatorAffiliationResearch TitleData in Use (Dataset ID)Period of Data Use
Kouya Shiraishi Division of Genome Biology, National Cancer Research Institute Elucidation of immune-system networks between host and tumor based on genomic analysis JGAD000311 2019/09/18-2023/03/31