Gut virome in pediatric VEO-IBD, USA
82 gut virome samples from children in Pennsylvania, USA, including Crohn's disease, IBD-unspecified, ulcerative colitis, and healthy controls, examining possible viral involvement in very early onset IBD disease processes. machine-written summary
82 samples · 82 runs · US · Child · 2020 · 0.53 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 768 sample values (antibiotic exposure, collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ✓ Abstract / description | 5 sample values (health condition) |
| – Full text | no open-access full text linked · PMC7648169 |
| – 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 |
antibiotic exposure: two sequence archives disagree for 4 samples (e.g. no vs yes) — withheld.
The sources disagree on 4 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (4)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN12730304 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN12730312 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN12730328 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN12730341 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
Genera, mean relative abundance over 19 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 | 82 | 100% | ||||
| country | 82 | 100% | 82 | |||
| health_condition | 82 | 100% | 77 | 5 | ||
| subject_id | 82 | 100% | 82 | |||
| collection_date | 82 | 100% | 82 | |||
| detailed_location | 82 | 100% | ||||
| health_condition_detail | 82 | 100% | 82 | |||
| latitude | 82 | 100% | 82 | |||
| location_region | 82 | 100% | 82 | |||
| longitude | 82 | 100% | 82 | |||
| antibiotic_exposure | 73 | 89% | 73 | |||
| medication | 22 | 27% | 22 | |||
| medication_detail | 22 | 27% | 22 |
- Dynamics of the Stool Virome in Very Early-Onset Inflammatory Bowel Disease. 2020 PMID 32406906 PMC7648169 own_data
Archive description
Here we focus on the viral portion of the virome to assess possible viral involvement in disease processes, reasoning that the possible influences of the virome might be more obvious in very early onset (VEO) IBD, which is defined as onset of IBD before 6 years of age.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child by opus_adjudicated with confidence 0.50. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “Gut virome in VEO-IBD”
- life stage study.description · “onset of IBD before 6 years of age”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN12730276 | antibiotic_exposure | no | R1 | 0.90 | biosample_attr | No |
| SAMN12730276 | collection_date | 2016-05-11 | R1 | 0.90 | biosample.attribute:collection_date | 2016-05-11 |
| SAMN12730276 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:PA |
| SAMN12730276 | health_condition | healthy_control | R1 | 0.90 | biosample_attr | Healthy |
| SAMN12730299 | health_condition | ibd_unspecified | R4 | 0.50 | study.description | very early onset (VEO) IBD |
| SAMN12730276 | health_condition_detail | Healthy | R1 | 0.90 | sample.attr.disease | Healthy |
| SAMN12730276 | latitude | 39.5700 | R1 | 0.90 | biosample.attribute:lat_lon | 39.57 N 75.13 W |
| SAMN12730276 | location_region | Pennsylvania | R1 | 0.75 | biosample.attribute:geo_loc_name | USA:PA |
| SAMN12730276 | longitude | -75.1300 | R1 | 0.90 | biosample.attribute:lat_lon | 39.57 N 75.13 W |
| SAMN12730304 | medication | corticosteroid;immunosuppressant_or_biologic | R1 | 0.85 | biosample.attribute:other_immunosuppression | prednisone |
| SAMN12730304 | medication_detail | prednisone | R1 | 0.85 | biosample.attribute:other_immunosuppression | prednisone |
| SAMN12730276 | subject_id | 1183 | R1 | 0.85 | sample.attr.subject_id | 1183 |
Sequencing
82 runs over 82 samples · mean 0.98 Gbp per run (median 0.53 Gbp, total 80.65 Gbp; 82 runs with a base count) · layout PAIRED 82 · platform ILLUMINA 82 · models Illumina HiSeq 2500 (82) · 23% of runs with a Sandpiper profile · first public 2020-04-26 – 2021-09-09
Authors (0)
No author record.
Downloads
PRJNA564995.csv.gz (3.8 KB) · parquet (75.6 KB) — all 82 samples, every field with route and confidence · PRJNA564995_determinations.csv.gz (7.0 KB) — 773 evidence rows