Gut microbiome in colonoscopy rinsates from IBD patients, USA
Shotgun metagenomic sequencing of 80 colonoscopic rinsate samples from US patients with Crohn's disease (n=50) or ulcerative colitis (n=15), examining microbiome patterns in inflammatory bowel disease. machine-written summary
80 samples · 80 runs · US · Age unknown · 2024 · 0.55 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 290 sample values (collection date, country, health condition, health condition detail) |
| – 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 · share metadata |
| – 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 | 80 | 100% | 80 | |||
| health_condition | 65 | 81% | 65 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 80 | 100% | 80 | |||
| health_condition_detail | 65 | 81% | 65 |
Archive description
The association between the microbiome and Inflammatory Bowel Disease by analyzing 80 colonscopy rinsate samples from intestinal microfistulous tracts, suggesting the potential influence of microbiome commensals on the inflammatory processes in Crohn's disease and Ulcerative colitis patients.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by curator_audit with confidence 0.60. Assay shotgun_dna.
- host runs.isolation_source · “Colonoscopic rinsates”
- host runs.scientific_name · “human gut metagenome”
- body site runs.isolation_source · “Colonoscopic rinsates”
- body site runs.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN39418236 | collection_date | 2021-06-07 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2021-06-07 |
| SAMN39418236 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Ohio, Cleveland |
| SAMN39418236 | health_condition | crohns_disease | R1 | 0.70 | sample.name_rule:library_names | CD_1 |
| SAMN39418236 | health_condition_detail | Crohn's disease | R1 | 0.70 | sample.name_rule:library_names | CD_1 |
Sequencing
80 runs over 80 samples · mean 0.65 Gbp per run (median 0.55 Gbp, total 51.83 Gbp; 80 runs with a base count) · layout PAIRED 80 · platform ILLUMINA 80 · models Illumina HiSeq X (80) · 10% of runs with a Sandpiper profile · first public 2024-04-28
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJNA1064103.csv.gz (2.7 KB) · parquet (72.4 KB) — all 80 samples, every field with route and confidence · PRJNA1064103_determinations.csv.gz (2.9 KB) — 290 evidence rows