Pediatric Crohn's ileal microbiome, Seoul
22 terminal ileal tissue samples from pediatric Crohn's disease patients and controls in Seoul, Korea, profiled by spatial host-microbiome sequencing and shotgun metagenomics in a case-control study. machine-written summary
22 samples · 22 runs · KR · Child · 2025 · 11.82 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 132 sample values (collection date, country, health condition, health condition detail, location region, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 44 sample values (location locality, location site) · PMC12374449 |
| ○ 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
8 of 8 people sampled more than once (22 samples; median 3, up to 3 per person).
Genera, mean relative abundance over 13 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 | 22 | 100% | ||||
| country | 22 | 100% | 22 | |||
| health_condition | 22 | 100% | 22 | |||
| subject_id | 22 | 100% | 22 | |||
| collection_date | 22 | 100% | 22 | |||
| detailed_location | 22 | 100% | ||||
| health_condition_detail | 22 | 100% | 22 | |||
| location_locality | 22 | 100% | 22 | |||
| location_region | 22 | 100% | 22 | |||
| location_site | 22 | 100% | 22 |
- Spatial host-microbiome profiling demonstrates bacterial-associated host transcriptional alterations in pediatric ileal Crohn's disease. 2025 PMID 40849632 PMC12374449 own_data
Archive description
We studied 14 terminal ileal tissue samples from six pediatric CD patients and two controls. Spatial host-microbiome sequencing. combining spatial transcriptomics with in-situ polyadenylation, and bulk shotgun metagenome sequencing were performed.
How this project entered the registry
Classified as human gut / stool mixed assays of child by sonnet_x2 with confidence 0.60. Assay mixed.
- host run.host_tax_id · “9606”
- body site study.description · “terminal ileal tissue samples from six pediatric CD patients”
- life stage study.title · “Pediatric Crohn's disease”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN43576368 | collection_date | 2022-12-13 | R1 | 0.90 | biosample.attribute:collection_date | 2022-12-13 |
| SAMN43576368 | country | KR | R1 | 0.90 | sample.attr.geo_loc_name | Korea: Seoul |
| SAMN43576368 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:sample_title | Ctrl |
| SAMN43576368 | health_condition_detail | Ctrl | R1 | 0.70 | sample.name_rule:sample_title | Ctrl |
| SAMN43576368 | location_locality | Seoul | R3 | 0.70 | paper.fulltext.methods | Sinchon Severance Hospital, in Seoul |
| SAMN43576368 | location_region | Seoul | R1 | 0.85 | biosample.attribute:geo_loc_name | Korea: Seoul |
| SAMN43576368 | location_site | Sinchon Severance Hospital | R3 | 0.70 | paper.fulltext.methods | patients with CD from the Sinchon Severance Hospital |
| SAMN43576368 | subject_id | Ctrl1 | R1 | 0.70 | sample.name_rule:sample_title | Ctrl1 |
Sequencing
22 runs over 22 samples · mean 11.74 Gbp per run (median 11.82 Gbp, total 258.19 Gbp; 22 runs with a base count) · layout PAIRED 22 · platform ILLUMINA 22 · models Illumina NovaSeq 6000 (22) · 68% of runs with a Sandpiper profile · first public 2025-09-03 – 2025-09-21
Downloads
PRJNA1159478.csv.gz (1.5 KB) · parquet (70.7 KB) — all 22 samples, every field with route and confidence · PRJNA1159478_determinations.csv.gz (1.9 KB) — 176 evidence rows