NBDC Research ID: hum0287.v3

 

SUMMARY

Aims: Genome sequence comparison of human iPS cell lines

Methods: Genomic DNA was extracted from human iPS cell lines and whole genome sequence analysis was performed.

Participants/Materials: Human iPS cell lines

 

Dataset IDType of DataCriteriaRelease Date
JGAS000310 NGS (Target Capture) Controlled-access (Type I) 2021/11/02
JGAS000573 NGS (Target Capture) Controlled-access (Type I) 2023/03/29
JGAS000690 NGS (Target Capture) Controlled-access (Type I) 2024/05/01

*Release Note 

*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

 

JGAS000310

Participants/Materials Human iPS cell line: 5 lines
Targets WGS
Target Loci for Capture Methods -
Platform Illumina [HiSeq X]
Library Source gDNAs extracted from iPS cells
Cell Lines -
Library Construction (kit name) TruSeq DNA PCR Free (350)
Fragmentation Methods Ultrasonic fragmentation (Covaris)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000421
Total Data Volume 343 GB (fastq)
Comments (Policies) NBDC policy

 

JGAS000573

Participants/Materials

Human iPS cell line: 1 line

    AGVT cell line (AG: TFAP2C-EGFP; VT: hVASA-tdTomato knock-ins)*1, *2

Targets WGS
Target Loci for Capture Methods -
Platform Nanopore [PromethION]
Library Source gDNAs extracted from iPS cells
Cell Lines -
Library Construction (kit name)

Ligation Sequencing Kit (SQK-LSK110) (run1)

Ultra-Long DNA Sequencing Kit (SQK-ULK001) (run2)

Fragmentation Methods transposase chemistry
Spot Type Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) N50 = 6.7 kb (run1) or 110 kb (run2)
Japanese Genotype-phenotype Archive Dataset ID JGAD000699
Total Data Volume 89.8 GB (fastq)
Comments (Policies) NBDC policy

 

JGAS000690

Participants/Materials

Human iPS cell line: 1 line

    AGVT cell line (AG: TFAP2C-EGFP; VT: hVASA-tdTomato knock-ins)*1, *2

Targets WGS
Target Loci for Capture Methods -
Platform Nanopore [PromethION]
Library Source gDNAs extracted from iPS cells
Cell Lines Human iPS cell line provided by RxCell Inc (NCL-CN)
Library Construction (kit name) Ultra-Long DNA Sequencing Kit (SQK-ULK001) (run1, run2)
Fragmentation Methods transposase chemistry
Spot Type Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) N50 = 80.7 kb (run1) or 96.3 kb (run2)
Japanese Genotype-phenotype Archive Dataset ID JGAD000823
Total Data Volume 83.2 GB (fastq)
Comments (Policies) NBDC policy

*1: doi:10.1126/science.aat1674

*2: doi:10.15252/embj.2020104929

 

DATA PROVIDER

Principal Investigator: Shihori Yokobayashi

Affiliation: Center for iPS Cell Research and Application, Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University

Project / Group Name: -

Funds / Grants (Research Project Number):

NameTitleProject Number
KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area) Chromatin dynamics linked to the epigenomic heterogeneity in human pluripotent stem cells 20H05387
KAKENHI Grant-in-Aid for Scientific Research (B) Chromatin dynamics during primordial germ cell development in mammals 18H02613
KAKENHI Grant-in-Aid for Specially Promoted Research Elucidation of the mechanism for human oocyte development based on its in vitro reconstitution 22H04920

 

PUBLICATIONS

TitleDOIDataset ID
1 Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells doi: 10.1016/j.celrep.2021.109909 JGAD000421
2 Induction of fetal meiotic oocytes from embryonic stem cells in cynomolgus monkeys doi: 10.15252/embj.2022112962 JGAD000699
3

 

USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use