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 IDType of DataCriteriaRelease Date

DRA006622

DRA007336

DRA008459

NGS (WGS) Unrestricted-access 2020/01/14
E-GEAD-311 SNP array Unrestricted-access 2020/01/14

*Release Note

*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

WGS

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

 

SNP array

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):

NameTitleProject 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

TitleDOIDataset 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