Fecal DNA extraction method comparison in Japanese adults
30 fecal samples from adults in Japan, used to assess and compare DNA extraction methods for shotgun metagenome sequencing (MiSeq); no health condition or intervention specified. machine-written summary
30 samples · 30 runs · JP · Adult · 2019 · 0.56 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 60 sample values (country, subject id) |
| – Abstract / description | no abstract or project description |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
3 of 3 people sampled more than once (30 samples; median 10, up to 10 per person).
Genera, mean relative abundance over 28 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 30 | 100% | ||||
| country | 30 | 100% | 30 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 30 | 100% | 30 |
Archive description
Method assessment of DNA extraction from 3 adults feces (Ogata et al). The shotgun genome sequence was carried out using MiSeq (illumina).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.description · “DNA extraction from 3 adults feces”
- life stage study.description · “DNA extraction from 3 adults feces”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00099620 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan |
| SAMD00099620 | subject_id | adult3 | R1 | 0.85 | sample.attr.host_subject_id | adult3 |
Sequencing
30 runs over 30 samples · mean 0.60 Gbp per run (median 0.56 Gbp, total 17.90 Gbp; 30 runs with a base count) · layout PAIRED 30 · platform ILLUMINA 30 · models Illumina MiSeq (30) · 93% of runs with a Sandpiper profile · first public 2019-11-20
Authors (0)
No author record.
Downloads
PRJDB6503.csv.gz (1.4 KB) · parquet (69.2 KB) — all 30 samples, every field with route and confidence · PRJDB6503_determinations.csv.gz (549 B) — 60 evidence rows