Bowel prep effects on endoscopic microbiome sampling in IBD
122 samples from IBD patients, comparing endoscopic microbiome sampling with and without standard bowel preparation in an intervention study design. machine-written summary
122 samples · 244 runs · GB · Age unknown · 2019 · 1.71 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 122 sample values (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 | 366 sample values (country, health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Bowel cleansing / colonoscopy preparation design observational_with_procedure · population ibd_unspecified · Endoscopy without vs with standard bowel preparation, same IBD patients
“one without standard bowel preparation, and another” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
Schedule stated by the source: “Two endoscopic procedures per patient: one without bowel preparation, followed a few days later by one with standard bowel preparation.” (time origin: First endoscopic procedure (without bowel preparation)).
Genera, mean relative abundance over 89 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 | 0 | 0% | ||||
| country | 122 | 100% | 122 | |||
| health_condition | 122 | 100% | 122 | |||
| subject_id | 122 | 100% | 122 | |||
| health_condition_detail | 122 | 100% | 122 |
Archive description
We are extending our pilot to study key factors about endoscopic sampling of the microbiome. These include sampling site, method and the "bowel preparation" typically done before endoscopy. To achieve this we will perform two separate procedures on a small number of IBD patients: one without standard bowel preparation, and another follow-up, with prep, a few days later.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.55. Assay shotgun_dna.
- host study.description · “a small number of IBD patients”
- body site study.description · “endoscopic sampling of the microbiome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104312992 | country | GB | R2 | 0.75 | external.gmrepo source | country: United Kingdom |
| SAMEA104312992 | health_condition | ibd_unspecified | R2 | 0.75 | external.gmrepo source | phenotype: Inflammatory Bowel Diseases |
| SAMEA104312992 | health_condition_detail | Inflammatory Bowel Diseases | R2 | 0.75 | external.gmrepo source | phenotype: Inflammatory Bowel Diseases |
| SAMEA104312992 | subject_id | GEM_PREP7082845 | R1 | 0.85 | sample.attr.subject_id | GEM_PREP7082845 |
Sequencing
244 runs over 122 samples · mean 0.82 Gbp per run (median 0.86 Gbp, total 200.48 Gbp; 244 runs with a base count) · layout PAIRED 244 · platform ILLUMINA 244 · models Illumina HiSeq 2500 (244) · 64% of runs with a Sandpiper profile · first public 2019-03-05 – 2020-06-30
Authors (0)
No author record.
Downloads
PRJEB22481.csv.gz (3.5 KB) · parquet (74.4 KB) — all 122 samples, every field with route and confidence · PRJEB22481_determinations.csv.gz (4.5 KB) — 488 evidence rows