Pediatric IBD gut mucosa metagenomes, multi-site, Canada
37 mucus swab samples from pediatric patients (24 Crohn's disease, 8 ulcerative colitis, plus non-IBD controls) in Canada, collected from appendix, peri-appendicular region, cecum, and ascending colon in a case-control design. machine-written summary
37 samples · 37 runs · CA · Child · 2025 · 9.15 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 328 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude, sex) |
| ○ 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 |
longitudinal — not resolved
9 of 9 people sampled more than once (18 samples; median 2, up to 2 per person).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 37 | 100% | ||||
| country | 37 | 100% | 37 | |||
| health_condition | 32 | 86% | 32 | |||
| subject_id | 37 | 100% | 37 | |||
| collection_date | 37 | 100% | 37 | |||
| detailed_location | 37 | 100% | ||||
| health_condition_detail | 37 | 100% | 37 | |||
| latitude | 37 | 100% | 37 | |||
| location_region | 37 | 100% | 37 | |||
| longitude | 37 | 100% | 37 | |||
| sex | 37 | 100% | 37 |
- Host-microbe interactions in the appendix of children with inflammatory bowel diseases. 2026 PMID 42531280 own_data
Archive description
Mucus samples from pediatric IBD patients and control non-IBD patients were collected from the appendix, peri-appendicular region, cecum, and ascending colon using sterile swabs immediately after excision. The samples were promptly frozen at -80C for subsequent DNA extraction and whole genome sequencing. Appendix tissues preserved in RNA-later were kept at room temperature for 1 hour before being frozen at -80C for DNA and RNA extraction, intended for 16S rRNA and RNA sequencing (GSE281635) respectively.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids / other human site shotgun DNA metagenome of child by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host study.title · “pediatric IBD patients”
- body site study.description · “appendix, peri-appendicular region, cecum, and ascending colon”
- body site sample.attr.isolation_source · “Appendix (n=10/37)”
- body site sample.attr.isolation_source · “Peri Appendix (n=9/37)”
- life stage study.title · “pediatric IBD patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN43761055 | collection_date | 2022 | R1 | 0.90 | biosample.attribute:collection_date | 2022 |
| SAMN43761055 | country | CA | R1 | 0.90 | sample.attr.geo_loc_name | Canada |
| SAMN43761057 | health_condition | ulcerative_colitis | R1 | 0.90 | biosample_attr | UC |
| SAMN43761055 | health_condition_detail | Non-IBD | R1 | 0.90 | sample.attr.ibdstatus | Non-IBD |
| SAMN43761055 | latitude | 53.5461 | R1 | 0.90 | biosample.attribute:lat_lon | 53.5461 N 113.4937 W |
| SAMN43761055 | location_region | Alberta | R1 | 0.60 | biosample.attribute:lat_lon | 53.5461 N 113.4937 W |
| SAMN43761055 | longitude | -113.4937 | R1 | 0.90 | biosample.attribute:lat_lon | 53.5461 N 113.4937 W |
| SAMN43761055 | sex | male | R1 | 0.90 | sample.attr.gender | male |
| SAMN43761055 | subject_id | N-IBD-2 | R1 | 0.70 | sample.name_rule:alias | Appx-2-N-IBD |
Sequencing
37 runs over 37 samples · mean 9.64 Gbp per run (median 9.15 Gbp, total 356.79 Gbp; 37 runs with a base count) · layout PAIRED 37 · platform ILLUMINA 37 · models Illumina NovaSeq 6000 (37) · 0% of runs with a Sandpiper profile · first public 2025-11-01
Authors (0)
No author record.
Downloads
PRJNA1160849.csv.gz (1.9 KB) · parquet (71.2 KB) — all 37 samples, every field with route and confidence · PRJNA1160849_determinations.csv.gz (2.7 KB) — 328 evidence rows