NBDC Research ID: hum0344.v1
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SUMMARY
Aims: To investigate genomic alterations of Japanese biliary tract cancer
Methods: Whole genome sequencing analysis and transcriptome sequencing analysis
Participants/Materials: Kidney cancer in endo-stage kidney disease
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000535 | Controlled-access (Type I) | 2022/08/04 |
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MOLECULAR DATA
| Participants/Materials |
Kidney cancer (ICD10: C64) in endo-stage kidney disease: 38 cases (of these, 26 cases also underwent RNA-seq analysis) tumor tissues: 38 samples non-tumor tissues/peripheral blood cells: 37 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | MGI Tech [MGISEQ-2000RS] |
| Library Source | DNAs extracted from tumor tissues and non-tumor tissues/peripheral blood cells from kidney cancer in endo-stage kidney disease |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Ultra II FS DNA Module and MGIEasy DNA library prep kit |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp or 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000652 |
| Total Data Volume | 9.1 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: |
Kidney cancer (ICD10: C64) in endo-stage kidney disease: 26 cases (These were also undergone WGS analysis) tumor tissues: 26 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from tumor tissues from kidney cancer in endo-stage kidney disease |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Stranded mRNA Library Prep Kit |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 126 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000652 |
| Total Data Volume | 9.1 TB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Hidewaki Nakagawa
Affiliation: Laboratory of Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences
Project / Group Name: Laboratory for Cancer Genomics
URL: https://www.riken.jp/en/research/labs/ims/genome_seq_anl/index.html
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| - | - | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Genomic features of renal cell carcinoma developed during end-stage renal disease and dialysis | doi: 10.1093/hmg/ddac180 | JGAD000652 |
| 2 |
USERS (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
