NBDC Research ID: hum0179.v1
SUMMARY
Aims: To reveal to what extent long-read data of PromethION deeps our understanding of oral microbiome and virome
Methods: Shutgun metagenome sequencing of bulk DNA extracted from saliva stored in OMNIgeneORAL OM-501 using a enzymatic method
Participants/Materials: Saliva of Japanese healthy individuals
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000186 | Metagenome | Controlled-access (Type I) | 2020/04/03 |
| DRA009794 | Metagenome | Unrestricted-access | 2020/04/03 |
* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
When the research results including the data which were downloaded from NHA/DRA/JGA, 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: | 4 healthy individuals |
| Targets | Metagenome |
| Target Loci for Capture Methods | - |
| Platform |
1. Nanopore [PromethION] 2. Illumina [HiSeq] |
| Library Source | DNA extracted from saliva |
| Cell Lines | - |
| Library Construction (kit name) |
1. ligation sequencing kit (SQK-LSK109) 2. Nextera XT |
| Fragmentation Methods | - |
| Spot Type |
1. Single-end 2. Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
1. variable, 13kb on average 2. 300 bp |
| Human Sequence removal Methods | EDGE pipeline |
| DDBJ Sequence Read Archive ID | DRA009794 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000268 |
| Total Data Volume |
1. 473 GB (fastq, txt) 2. 186 GB (fastq) |
| Comments (Policies) | NBDC policy |
*This study was supported by "Genome Science". "Genome Science" is a part of the "Support Programs for Three Fields in Life Sciences (cancer, genome, and brain sciences)" established by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) under the Grant-in-Aid for Scientific Research on Innovative Areas.
DATA PROVIDER
Principal Investigator: Koji Yahara
Affiliation: Antimicrobial Resistance Research Center, National Institute of Infectious Diseases
Project / Group Name: Neo-virology
URL: http://neo-virology.org/en/
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Big data analysis of bacteriophages and host bacterial using the extended virome datasets and long-read sequencer | 19H04846 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Long-read metagenomics using PromethION uncovers novel oral bacteriophages, their abundance, and interaction with host bacteria | doi: 10.1038/s41467-020-20199-9 | JGAS000186 DRA009794 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
