Gut metagenomes in liver disease vs healthy controls, Japan
Case-control study of 68 fecal WGS samples from liver disease patients and healthy controls in Kanazawa, Japan, examining gut microbiota composition. machine-written summary
68 samples · 68 runs · JP · Age unknown · 2019 · 0.52 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 498 sample values (collection date, country, health condition, health condition detail, latitude, location locality, longitude, subject id) |
| ✓ Abstract / description | 23 sample values (health condition detail) |
| ○ Full text | read; no usable statement or table · PMC12390848 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 68 | 100% | 68 | |||
| health_condition | 45 | 66% | 45 | |||
| subject_id | 68 | 100% | 68 | |||
| collection_date | 68 | 100% | 68 | |||
| detailed_location | 68 | 100% | ||||
| health_condition_detail | 68 | 100% | 45 | 23 | ||
| latitude | 68 | 100% | 68 | |||
| location_locality | 68 | 100% | 68 | |||
| longitude | 68 | 100% | 68 |
- Microbiota-driven antitumour immunity mediated by dendritic cell migration. 2025 PMID 40659786 PMC12390848 unsure
Archive description
WGS of fecal DNA obtained from liver disease patients and healthy controls
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “fecal DNA obtained from liver disease patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN10845506 | collection_date | 2013-08-30 | R1 | 0.90 | biosample.attribute:collection_date | 2013-08-30 |
| SAMN10845506 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan: Kanazawa |
| SAMN10845506 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:library_names | HD1 |
| SAMN10845506 | health_condition_detail | HD | R1 | 0.70 | sample.name_rule:library_names | HD1 |
| SAMN10845535 | health_condition_detail | mixed_case_control: Cohort includes both liver disease patients and healthy controls; no single condition applies to all | R4 | 0.50 | study.description | liver disease patients and healthy controls |
| SAMN10845506 | latitude | 36.5500 | R1 | 0.90 | biosample.attribute:lat_lon | 36.55 N 136.67 E |
| SAMN10845506 | location_locality | Kanazawa | R1 | 0.85 | biosample.attribute:geo_loc_name | Japan: Kanazawa |
| SAMN10845506 | longitude | 136.6700 | R1 | 0.90 | biosample.attribute:lat_lon | 36.55 N 136.67 E |
| SAMN10845506 | subject_id | HD1 | R1 | 0.85 | biosample.attribute:library_names | library_names: HD1 |
Sequencing
68 runs over 68 samples · mean 0.53 Gbp per run (median 0.52 Gbp, total 36.10 Gbp; 68 runs with a base count) · layout PAIRED 68 · platform ILLUMINA 68 · models Illumina MiSeq (68) · 0% of runs with a Sandpiper profile · first public 2019-02-01 – 2021-03-13
Authors (43)
Tarracchini C first · Lugli GA · Mancabelli L · van Sinderen D · Turroni F · Ventura M · Milani C last · Lin NY first · Fukuoka S · Koyama S · Motooka D · Tourlousse DM · Shigeno Y · Matsumoto Y · Yamano H · Murotomi K · Tamaki H · Irie T · Sugiyama E · Kumagai S · Itahashi K · Tanegashima T · Fujimaki K · Ito S · Shindo M · Tsuji T · Wake H · Watanabe K · Maeda Y · Enokida T · Tahara M · Yamashita R · Fujisawa T · Nomura M · Kawazoe A · Goto K · Doi T · Shitara K · Mano H · Sekiguchi Y · Nakamura S · Benno Y · Nishikawa H last
Downloads
PRJNA517801.csv.gz (2.9 KB) · parquet (73.6 KB) — all 68 samples, every field with route and confidence · PRJNA517801_determinations.csv.gz (5.0 KB) — 521 evidence rows