IgG-Bound Gut Bacteria in Pediatric IBD, Case-Control
42 samples from pediatric terminal ileum aspirate washes, comparing IgG-bound and -unbound bacteria across non-IBD, Crohn disease, and ulcerative colitis children; case-control design. machine-written summary
42 samples · 42 runs · CA · Child · 2019 · 0.20 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 126 sample values (health condition, health condition detail, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 126 sample values (country, location locality, location region) · PMC6317230 |
| ○ 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
14 of 14 people sampled more than once (42 samples; median 3, up to 3 per person).
Genera, mean relative abundance over 33 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 | 42 | 100% | ||||
| country | 42 | 100% | 42 | |||
| health_condition | 42 | 100% | 42 | |||
| subject_id | 42 | 100% | 42 | |||
| detailed_location | 42 | 100% | ||||
| health_condition_detail | 42 | 100% | 42 | |||
| location_locality | 42 | 100% | 42 | |||
| location_region | 42 | 100% | 42 |
- Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases. 2019 PMID 30606251 PMC6317230 own_data
Archive description
We hypothesized host immunoglobulin (Ig)G can be used to identify bacteria involved in IBD pathogenesis. IgG-bound and -unbound microorganisms were collected from 39 pediatric terminal ileum aspirate washes [non-IBD (n=10), CD (n=15), and UC (n=9)] and composition was assessed by next generation sequencing.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “human metagenome”
- body site study.description · “pediatric terminal ileum aspirate washes”
- life stage study.title · “Pediatric Inflammatory Bowel Diseases”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN09643466 | country | CA | R3 | 0.70 | paper.fulltext.methods | Stollery Children’s Hospital, University of Alberta in Edmonton, Alberta |
| SAMN09643466 | health_condition | crohns_disease | R1 | 0.70 | sample.name_rule:alias | CD-shotgun-133-IgG |
| SAMN09643466 | health_condition_detail | CD | R1 | 0.70 | sample.name_rule:alias | CD-shotgun-133-IgG |
| SAMN09643466 | location_locality | Edmonton | R3 | 0.70 | paper.fulltext.methods | Stollery Children's Hospital, University of Alberta in Edmonton, Alberta |
| SAMN09643466 | location_region | Alberta | R3 | 0.70 | paper.fulltext.methods | Stollery Children's Hospital, University of Alberta in Edmonton, Alberta |
| SAMN09643466 | subject_id | CD-shotgun-133 | R1 | 0.70 | sample.name_rule:alias | CD-shotgun-133-IgG |
Sequencing
42 runs over 42 samples · mean 0.20 Gbp per run (median 0.20 Gbp, total 8.58 Gbp; 42 runs with a base count) · layout PAIRED 42 · platform ILLUMINA 42 · models Illumina MiSeq (42) · 79% of runs with a Sandpiper profile · first public 2019-08-12
Authors (18)
Armstrong H first · Alipour M · Valcheva R · Bording-Jorgensen M · Jovel J · Zaidi D · Shah P · Lou Y · Ebeling C · Mason AL · Lafleur D · Jerasi J · Wong GK · Madsen K · Carroll MW · Huynh HQ · Dieleman LA · Wine E last
Downloads
PRJNA480674.csv.gz (1.7 KB) · parquet (70.6 KB) — all 42 samples, every field with route and confidence · PRJNA480674_determinations.csv.gz (2.5 KB) — 252 evidence rows