NBDC Research ID: hum0484.v1
SUMMARY
Aims: The purpose is to contribute to the development of various fields of life science by providing human iPS cell lines to researchers who use them. Established human iPS cell lines will be deposited and transferred to the RIKEN BioResource Research Center (BRC), which will manage and supervise them under the cell quality control system. In this project, various characteristic analyses will be carried out to enhance the value of the samples by enriching the cell characteristics. Genetic information is crucial for sample quality control, so genetic analysis will be conducted to increase the value of the samples and provided as cell accompanying information.
Methods: Whole genome sequencing
Participants/Materials: iPS cell lines derived from peripheral blood cells or skin tissues of patients with amyotrophic lateral sclerosis (ALS).
URL: https://cell.brc.riken.jp/en/
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000775 | NGS (WGS) | Controlled-access (Type I) | 2025/02/17 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
ALS (ICD10: G12.2): 33 cases iPS cell lines derived from peripheral blood cells or skin rissues: 33 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from iPS cell lines |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq DNA PCR-Free Library Prep kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 151 bp |
| Mapping Methods | iSAAC aligner (iSAAC-04.18.11.09) |
| Mapping Quality | [0, 2^8-1] |
| Reference Genome Sequence | hg38 |
| Coverage (Depth) | 25.72-30.34 |
| Detecting Methods for Variation | Strelka (2.9.10), Manta (1.5.0), Control-FREEC (11.5) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000917 |
| Total Data Volume | 2.5 TB (fastq, bam, bai, vcf, tabix) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Yukio Nakamura
Affiliation: RIKEN BioResource Research Center
Project / Group Name: Cell Engineering Division
URL: https://cell.brc.riken.jp/en/
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | |||
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
