Bile acid metabolism in UC vs FAP ileal pouches
10 stool samples from colectomy patients with ileal pouches (ulcerative colitis vs familial adenomatous polyposis controls), a case-control study of secondary bile acid deficiency and intestinal inflammation; country not reported. machine-written summary
10 samples · 10 runs · Adult · 2020 · 7.67 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 40 sample values (age, health condition, health condition detail, sex) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC8172352 |
| – 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 |
intervention — arms not resolved
Surgical procedure studied before/after (bariatric surgery design observational_with_procedure · population ulcerative_colitis · colectomy with ileal pouch creation in UC/FAP patients
“colectomy-treated patients with ulcerative colitis” — abstract:32101703 (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 8 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 | 10 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 10 | 100% | 10 | |||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 10 | 100% | 10 | |||
| health_condition_detail | 10 | 100% | 10 | |||
| sex | 10 | 100% | 10 |
- Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation. 2020 PMID 32101703 PMC8172352 unsure
Archive description
bacterial genes associated to bai operon are important in converting primary bile acid to secondary bile acid. the aim is to involve BAI expression in UC pouch.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human gut metagenome”
- life stage sample.attr.age · “22 (n=8/10)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN13763797 | age_at_collection_days | 21549.8 | R1 | 0.70 | sample.attr.age | 59 |
| SAMN13763797 | health_condition | ibd_unspecified | R1 | 0.85 | biosample.attribute:TITLE | TITLE: IBD |
| SAMN13763797 | health_condition_detail | IBD | R1 | 0.85 | biosample.attribute:TITLE | TITLE: IBD |
| SAMN13763797 | sex | male | R1 | 0.90 | sample.attr.sex | male |
Sequencing
10 runs over 10 samples · mean 7.72 Gbp per run (median 7.67 Gbp, total 77.16 Gbp; 10 runs with a base count) · layout PAIRED 10 · platform ILLUMINA 10 · models Illumina HiSeq 2500 (10) · 80% of runs with a Sandpiper profile · first public 2020-01-09
Authors (15)
Sinha SR first · Haileselassie Y · Nguyen LP · Tropini C · Wang M · Becker LS · Sim D · Jarr K · Spear ET · Singh G · Namkoong H · Bittinger K · Fischbach MA · Sonnenburg JL · Habtezion A last
Downloads
PRJNA600008.csv.gz (1.2 KB) · parquet (69.4 KB) — all 10 samples, every field with route and confidence · PRJNA600008_determinations.csv.gz (857 B) — 40 evidence rows