NBDC Research ID: hum0174.v2
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SUMMARY
Aims: To build a database of genomic structural variants in Japanese population
Methods: We sequenced genomic DNAs using PacBio and 10X Genomics sequencing technologies, and analyzed genomic structural variations.
Participants/Materials: Japanese (collected by Japanese B cell DNA bank)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000173 | NGS (WGS): Sequence raw data, Structural Variants data for each sample | Controlled-access (Type I) | 2020/10/06 |
| JGAS000173 (Data addition) | NGS (WGS) | Controlled-access (Type I) | 2020/11/27 |
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MOLECULAR DATA
| Participants/Materials: | Purified DNA from Japanese-origin B cell liens: 10 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform |
1. PacBio [Sequel] 2. 10x Genomics [Chromium Controller] |
| Library Source | Purified DNA from Japanese-origin B cell liens |
| Cell Lines | the Health Science Research Resources Bank (HSRRB), the National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) |
| Library Construction (kit name) |
1. the library prep. kit for SMRT sequencing by Pacific Biosciences 2. 10X Genomics-Chromium system |
| Fragmentation Methods |
1. Megaruptor, g-tube 2. None |
| Spot Type |
1. Single-end 2. Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
1. 14000 bp 2. 151 bp |
| QC Methods |
1. Qubit, Pulsed-field gel electrophoresis, TapeStation, Bioanalyzer 2. qPCR, Bioanalyzer |
| Mapping Methods |
1. minimap2 2. longranger by 10X Genomics |
| Depth (average) |
1. 29x 2. 19x |
| Structural Variants Detection Methods |
1. Sniffles 2. longranger by 10X Genomics |
| Polymorphism Number (after QC) |
1. 16870/sample 2. 11700/sample |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000251 |
| Total Data Volume | 1 TB (fastq, bam [ref: unmapped], bed, vcf [ref: hg38]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | Purified DNA from Japanese-origin B cell liens: 11 samples |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | PacBio [Sequel] |
| Library Source | Purified DNA from Japanese-origin B cell liens |
| Cell Lines | the Health Science Research Resources Bank (HSRRB), the National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) |
| Library Construction (kit name) | the library prep. kit for SMRT sequencing by Pacific Biosciences |
| Fragmentation Methods | Megaruptor, g-tube |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 14000 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000251 |
| Total Data Volume | 3.44 TB (bam) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shinichi Morishita
Affiliation: Graduate School of Frontier Sciences, the University of Tokyo
Project / Group Name： -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Advanced Genome Research and Bioinformatics Study to Facilitate Medical Innovation, Platform Program for Promotion of Genome Medicine, Japan Agency for Medical Research and Development (AMED) | Informatics for analyzing de novo human genome assemblies | 16km0405204h0001 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Rapid and ongoing evolution of repetitive sequence structures in human centromeres. | doi: 10.1126/sciadv.abd9230 | JGAD000251 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
