Colonic mucosal virome in pediatric Crohn's disease, Ottawa
16 samples from proximal and distal colon mucosal-luminal interface of pediatric Crohn's disease patients (Ottawa, Canada), analyzed by virus-like particle enrichment and whole metagenome sequencing in a cross-sectional design. machine-written summary
16 samples · 24 runs · CA · Child · 2020 · 1.60 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 160 sample values (age, collection date, country, health condition, health condition detail, latitude, location locality, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 48 sample values (antibiotic exposure, location region, location site) · PMC7642909 |
| ○ 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 |
longitudinal — not resolved
5 of 5 people sampled more than once (16 samples; median 4, up to 4 per person).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 16 | 100% | ||||
| country | 16 | 100% | 16 | |||
| health_condition | 16 | 100% | 16 | |||
| subject_id | 16 | 100% | 16 | |||
| age_at_collection_days | 16 | 100% | 16 | |||
| antibiotic_exposure | 16 | 100% | 16 | |||
| collection_date | 16 | 100% | 16 | |||
| detailed_location | 16 | 100% | ||||
| health_condition_detail | 16 | 100% | 16 | |||
| latitude | 16 | 100% | 16 | |||
| location_locality | 16 | 100% | 16 | |||
| location_region | 16 | 100% | 16 | |||
| location_site | 16 | 100% | 16 | |||
| longitude | 16 | 100% | 16 | |||
| sex | 16 | 100% | 16 |
- Virome Sequencing of the Human Intestinal Mucosal-Luminal Interface. 2020 PMID 33194818 PMC7642909 own_data
Archive description
Virome and metagenome sequencing of the human mucosal-luminal interface from five pediatric subjects with Crohn's disease. Samples were obtained from the proximal and distal colon during colonoscopy and subjected to 1) virus-like particle enrichment and sequencing 2) whole metagenome sequencing.
How this project entered the registry
Classified as human gut / stool mixed assays of child and adolescent by sonnet_x2 with confidence 0.68. Assay mixed.
- host run.host_tax_id · “9606”
- body site study.description · “human mucosal-luminal interface”
- life stage study.description · “five pediatric subjects with Crohn's disease”
- life stage sample.attr.host_age · “13 (n=10/16)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN15522306 | age_at_collection_days | 5844.0 | R1 | 0.70 | sample.attr.host_age | 16 |
| SAMN15522306 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | antibiotic treatment in the past 4 weeks were excluded |
| SAMN15522306 | collection_date | 2018-07-16 | R1 | 0.90 | biosample.attribute:collection_date | 2018-07-16 |
| SAMN15522306 | country | CA | R1 | 0.90 | sample.attr.geo_loc_name | Canada: Ottawa |
| SAMN15522306 | health_condition | crohns_disease | R1 | 0.85 | biosample.attribute:gastrointest_disord | Crohn's disease |
| SAMN15522306 | health_condition_detail | Crohn's disease | R1 | 0.90 | sample.attr.gastrointest_disord | Crohn's disease |
| SAMN15522306 | latitude | 45.5000 | R1 | 0.90 | biosample.attribute:lat_lon | 45.50 N 75.65 W |
| SAMN15522306 | location_locality | Ottawa | R1 | 0.85 | biosample.attribute:geo_loc_name | Canada: Ottawa |
| SAMN15522306 | location_region | Ontario | R3 | 0.70 | paper.fulltext.methods | Children's Hospital of Eastern Ontario (CHEO) in Ottawa, Canada |
| SAMN15522306 | location_site | Children's Hospital of Eastern Ontario | R3 | 0.70 | paper.fulltext.methods | Children's Hospital of Eastern Ontario (CHEO) in Ottawa, Canada |
| SAMN15522306 | longitude | -75.6500 | R1 | 0.90 | biosample.attribute:lat_lon | 45.50 N 75.65 W |
| SAMN15522306 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN15522306 | subject_id | A | R1 | 0.70 | sample.name_rule:alias | A-PC-VIROME |
Sequencing
24 runs over 16 samples · mean 1.48 Gbp per run (median 1.49 Gbp, total 35.56 Gbp; 24 runs with a base count) · layout SINGLE 24 · platform ION_TORRENT 24 · models Ion Torrent Proton (24) · 0% of runs with a Sandpiper profile · first public 2020-10-09
Downloads
PRJNA645218.csv.gz (1.4 KB) · parquet (71.7 KB) — all 16 samples, every field with route and confidence · PRJNA645218_determinations.csv.gz (2.3 KB) — 208 evidence rows