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 ID | Type of Data | Criteria | Release 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 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
| 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 |
| 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 |
| 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):
| Name | Title | Project 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
| Title | DOI | Dataset 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 Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
