NBDC Research ID: hum0106.v1
SUMMARY
Aims: analysis of cellular diversity and hierarchy of human colorectal cancer (CRC)
Methods: single cell RNA-seq
Participants/Materials: culture tissues derived from CRC patients
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000139 | NGS (scRNA-seq) | Controlled-access (Type I) | 2022/09/05 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
CRC (ICD10: C18) patients 5 tumor tissues derived from 2 CRC patients (HCT24, HCT25) (2 cells from HCT24 and 3 cells from HCT25) non-tumor tissues derived from 1 CRC patient (HCT71) |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from single cells of culture tissues derived from CRC patients |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Single Cell 3' v1 Reagent kit |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 50 bp [Read1(transcript) 50bp, Read2(UMI) 15bp, Index1(CellBarcode) 14bp and Index2 (Sample Index) 8bp] |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000208 |
| Total Data Volume | 44 GB (fastq) |
| Comments (Policies) | NBDC policy |
This study was supported by “Genome Science”. “Genome Science” is a part of the “Support Programs for Three Fields in Life Sciences (cancer, genome and brain sciences)” established by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) under the Grant-in-Aid for Scientific Research on Innovative Areas.
DATA PROVIDER
Principal Investigator: Ryoji Yao
Affiliation: The Cancer Institute of JFCR
Project / Group Name: project orgnaoid
URL: https://www.jfcr.or.jp/laboratory/department/cell_biology/www/index.html
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Challenging Exploratory Research | Analysis of cellular heterogeneity of colorectal cancer | 16K14620 |
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Platform for advanced genome science | 16H06279 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Comparative Analysis of Patient-Matched PDOs Revealed a Reduction in OLFM4-Associated Clusters in Metastatic Lesions in Colorectal Cancer | doi: 10.1016/j.stemcr.2021.02.012 | JGAD000208 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
