NBDC Research ID: hum0277.v2
Click to Latest version.
SUMMARY
Aims: To clarify the oncogenesis and the progression mechanisms of urological tumors, we performed comprehensive epi-genetic analyses. Through the analyses, we aim for elucidating the oncogenesis or for developing new treatment strategies for each cancer.
Methods: single-cell RNA sequencing (scRNA-seq), whole exome sequencing (WES), and RNA-seq
- scRNA-seq: We sliced surgically resected specimens and minced and digested into the single cell level. Libraries were prepared using Chromium single cell 3’ kit (10X Genomics) according to the manufacturer’s protocol. Paired-end sequencing was conducted on the NextSeq 500 platform (Illumina).
- WES: Libraries were prepared using SureSelect Human All Exon V6 (Agilent Technologies) and sequenced by using of NovaSeq 6000/PE150 (Illumina).
- RNA-seq: Libraries were prepared using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA CD Index Kit (Dual Index) and sequenced by using of HiSeq 2500 (Illumina).
- WGS: Genomic DNAs were extracted from frozen tissues. The library construction was done using the TruSeq Nano DNA Library Prep Kit and sequenced by using of NovaSeq 6000 (Illumina).
Participants/Materials: 19 patients with Birt-Hogg-Dubé (BHD) associated renal cell carcinoma (RCC), 1 patient with hereditary leiomyomatosis and renal cell cancer (HLRCC) associated RCC, 2 patients with Von Hippel-Lindau (VHL) associated RCC, 2 patients with sporadic clear cell RCC (ccRCC), and 21 patients with sporadic chromophobe RCC (chRCC)
- scRNA-seq: 2 BHD-associated RCC, 1 HLRCC-associated RCC, 2 VHL-associated RCC, and 2 ccRCC
- WES: 2 BHD-associated RCC, 1 HLRCC-associated RCC, 2 VHL-associated RCC, and 2 ccRCC
- RNA-seq: 10 BHD-associated RCC and 21 chRCC
- WGS: 9 BHD-associated RCC
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000303 | NGS (scRNA-seq, Exome, RNA-seq) | Controlled-access (Type I) | 2022/09/09 |
| JGAS000564 | NGS (WGS, RNA-seq) | Controlled-access (Type I) | 2023/04/18 |
* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
RCC (ICD10: C64): 7 cases BHD (ICD10: Q878) -associated RCC: 2 cases (2 samples) HLRCC (MedGen ID: 353771) -associated RCC: 1 case (2 samples) VHL (ICD10: Q858) -associated RCC: 2 cases (2 samples) ccRCC: 2 cases (4 tumor samples and 2 normal kidney tissues) |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000/NextSeq 500] |
| Library Source | RNAs extracted from single cells of tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Chromium single cell 3’ kit (10XGenomics) |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | index 8 bp, read1 28 bp, read2 91 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000414 |
| Total Data Volume | 316.9 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
RCC (ICD10: C64): 7 cases BHD (ICD10: Q878) -associated RCC: 2 cases (tumor: 2 samples, normal kidney: 2 samples) HLRCC (MedGen ID: 353771) -associated RCC: 1 case (tumor: 2 samples, normal kidney: 1 sample) VHL (ICD10: Q858) -associated RCC: 2 cases (tumor: 2 samples, normal kidney: 2 samples) ccRCC: 2 cases (tumor: 4 samples, normal kidney: 2 samples) |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000/PE150] |
| Library Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon V6 (Agilent Technologies) |
| Fragmentation Methods | Ultrasonic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | read1 150 bp, read2 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000414 |
| Total Data Volume | 316.9 GB (fastq) |
| Comments (Policies) | NBDC policy |
RNA-seq (JGAS000303, JGAS000564)
| Participants/Materials |
BHD (ICD10: Q878) -associated RCC (ICD10: C64): 10 cases (tumor: 16 samples, normal kidney: 5 samples) chRCC (ICD10: C64): 21 cases (tumor: 21 samples) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Stranded mRNA Library Prep Kit, TruSeq RNA CD Index Kit (Dual Index) |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | read1 126 bp, read2 126 bp |
| Japanese Genotype-phenotype Archive Dataset ID | |
| Total Data Volume |
JGAD000414: 316.9 GB (fastq) JGAD000686: 1.4 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
BHD (ICD10: Q878) -associated RCC (ICD10: C64): 9 cases (tumor: 16 samples, normal kidney: 9 samples) |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Nano DNA Library Prep Kit (Illumina) |
| Fragmentation Methods | Ultrasonic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | read1 150 bp, read2 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000686 |
| Total Data Volume | 1.4 TB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Hisashi Hasumi
Affiliation: Department of Urology, Yokohama City University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Analysis on the mechanism of renal tumorigenesis focusing on the metabolic and membrane transport regulation of FLCN | 19K09694 |
| the MEXT Joint Usage/Research Center Program | The Advanced Medical Research Center of Yokohama City University "Center for Advanced Medical Research Collaboration in Multi-omics Gene Expression Regulation" |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Single-cell transcriptomes underscore genetically distinct tumor characteristics and microenvironment for hereditary kidney cancers | doi: 10.1016/j.isci.2022.104463 | JGAD000414 |
| 2 | Comparative analyses define differences between BHD-associated renal tumour and sporadic chromophobe renal cell carcinoma | doi: 10.1016/j.ebiom.2023.104596 | JGAD000686 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
