NBDC Research ID: hum0122.v1
SUMMARY
Aims: Elucidation of genome instability during genome reprogramming
Methods: Whole genome sequencing and copy number variation analysis using SNP array of iPS cells and their parental cells to identify genetic abberations
Participants/Materials: Human iPS cells derived from commercially-available primary cells
URL: https://www.qst.go.jp/site/qst-english/
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
|
DRA006622 DRA007336 DRA008459 |
NGS (WGS) | Unrestricted-access | 2020/01/14 |
| E-GEAD-311 | SNP array | Unrestricted-access | 2020/01/14 |
*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
| Participants/Materials |
Mononuclear Cells from Cord Blood (Takara D10118): 4 sample (CB_1, CB_2-1, CB_2-2, and CB_2-3) - iPS cells derived from CB_1: 5 samples - iPS cells derived from CB_2-1: 3 samples - iPS cells derived from CB_2-2: 3 samples - iPS cells derived from CB_2-3: 3 samples Human Dermal Fibroblast (KURABO KF4109): 1 sample (adult human dermal fibroblast [HDFa]) - iPS cells derived from HDFa: 8 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq X Ten] |
| Library Source | DNAs extracted from iPS cells and their parental cells |
| Cell Lines |
TaKaRa Bio (D10118): http://catalog.takara-bio.co.jp/product/basic_info.php?unitid=U100007076 KURABO (KF4109): https://www.kurabo.co.jp/bio/product/products.php?M=L&A=C&PPID=118 |
| Library Construction (kit name) | TruSeq DNA PCR-Free Library Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 400 bp |
| DDBJ Sequence Read Archive ID |
DRA006622 (CB_1) DRA007336 (HDFa) DRA008459 (CB_1, CB_2-1, CB_2-2, CB_2-3) |
| Total Data Volume | 2 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Mononuclear Cells from Cord Blood (Takara D10118): 1 sample (CB_1) - iPS cells derived from CB_1: 4 samples Human Dermal Fibroblast (KURABO KF4109): 1 sample (HDFa) - iPS cells derived from HDFa: 2 samples |
| Targets | genome wide SNVs/CNVs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Infinium Omni2.5-8 v1.4 BeadChip] |
| Source | DNAs extracted from iPS cells and their parental cells |
| Cell Lines |
TaKaRa Bio (D10118): http://catalog.takara-bio.co.jp/product/basic_info.php?unitid=U100007076 KURABO (KF4109): https://www.kurabo.co.jp/bio/product/products.php?M=L&A=C&PPID=118 |
| Reagents (Kit, Version) | Infinium Omni2.5-8 v1.4 BeadChip Kit |
| Genotype Call Methods (software) | GenomeStudio (Illumina) |
| Marker number | About 2,500,000 CNVs |
| Genomic Expression Archive Dataset ID | E-GEAD-311 |
| Total Data Volume | 1 GB (idat, txt) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Ryoko Araki and Masumi Abe
Affiliation: National Institutes for Quantum and Radiological Science and Technology, National Institute of Radiological Sciences, Department of Basic Medical Sciences for Radiation Damages
Project / Group Name: Stem cell biology group
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (B) | Point mutations associated with genome reprogramming | 17H03615 |
| KAKENHI Grant-in-Aid for challenging Exploratory Research | Development of genome-wide analysis for radiation effects | 17K20053 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Genetic aberrations in iPSCs are introduced by a transient G1/S cell cycle checkpoint deficiency | doi: 10.1038/s41467-019-13830-x |
DRA006622 DRA007336 DRA008459 E-GEAD-311 |
| 2 |
