Stool metagenome in PSC patients vs matched controls (USA)
490 stool samples from USA adults, comprising 245 patients with primary sclerosing cholangitis and 245 age- and sex-matched controls, analyzed by shotgun metagenomic sequencing in a case-control design. machine-written summary
490 samples · 490 runs · US · Adult · 2026 · 1.50 Gbp / sample · cohort Compositional and functional differences of gut mi
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,430 sample values (country, health condition, health condition detail, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| – 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 |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 490 | 100% | ||||
| country | 490 | 100% | 490 | |||
| health_condition | 490 | 100% | 490 | |||
| subject_id | 490 | 100% | 490 | |||
| detailed_location | 490 | 100% | ||||
| health_condition_detail | 490 | 100% | 490 | |||
| latitude | 490 | 100% | 490 | |||
| location_region | 490 | 100% | 490 | |||
| longitude | 490 | 100% | 490 |
- Compositional and functional differences of gut microbiome and metabolome inform pathogenesis of cholestatic liver disease. 2026 PMID 41975274 PMC13078198 unsure
Archive description
Stool metagenomic sequencing of patients with PSC and controls. The cohort comprised of: 245 patients with primary sclerosing cholangitis (PSC), 245 age and sex matched PSC controls.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.title · “Stool metagenome in primary sclerosing cholangitis”
- life stage study.description · “245 patients with primary sclerosing cholangitis”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN55414796 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN55414796 | health_condition | liver_disease | R1 | 0.85 | biosample_attr | PSC |
| SAMN55414796 | health_condition_detail | primary sclerosing cholangitis (cholestatic liver disease) | R1 | 0.85 | biosample.attribute:group | PSC |
| SAMN55414796 | latitude | 44.0228 | R1 | 0.90 | biosample.attribute:lat_lon | 44.02275279 N 92.46684038 W |
| SAMN55414796 | location_region | Minnesota | R1 | 0.60 | biosample.attribute:lat_lon | 44.02275279 N 92.46684038 W |
| SAMN55414796 | longitude | -92.4668 | R1 | 0.90 | biosample.attribute:lat_lon | 44.02275279 N 92.46684038 W |
| SAMN55414796 | subject_id | PSC_patient_1 | R1 | 0.70 | sample.name_rule:TITLE | PSC_patient_1 |
Sequencing
490 runs over 490 samples · mean 1.52 Gbp per run (median 1.50 Gbp, total 743.19 Gbp; 490 runs with a base count) · layout PAIRED 490 · platform ILLUMINA 490 · models Illumina NovaSeq 6000 (490) · 0% of runs with a Sandpiper profile · first public 2026-05-05
Authors (29)
Nikolaidis M first · Hu C · Juran BD · McCauley BM · Schlicht EM · Bianchi JK · Ali AH · Tragaki V · Atkinson EJ · Johnson S · Mars RA · Eaton JE · Carey EJ · Franke A · Schramm C · Kashyap PC · Go YM · Tran V · Teeny S · Jones DP · Grant CW · Athreya AP · Miller GW · LaRusso NF · Gores GJ · Karlsen TH · Hov JR · Amoutzias GD · Lazaridis KN last
Downloads
PRJNA1425460.csv.gz (12.7 KB) · parquet (89.7 KB) — all 490 samples, every field with route and confidence · PRJNA1425460_determinations.csv.gz (21.5 KB) — 3,430 evidence rows