Gut virome in IBD patients and healthy controls, USA
Cross-sectional study of 96 gut virome samples from Pennsylvania, USA, comparing 86 samples from IBD (unspecified type) patients to 10 from healthy controls. machine-written summary
86 samples · 96 runs · US · Age unknown · 2021 · 1.38 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 766 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude, subject id) |
| – Abstract / description | no abstract or project description |
| – 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
43 of 43 people sampled more than once (86 samples; median 2, up to 2 per person) · follow-up median 7 mo (max 16 mo) · median interval between samples 7 mo (time from collection dates). Schedule stated by the source: “archive time labels: 01, 02, 03”.
Each row is one person (36 shown of 43); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 30 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 | 0 | 0% | ||||
| country | 86 | 100% | 86 | |||
| health_condition | 86 | 100% | 86 | |||
| subject_id | 86 | 100% | 86 | |||
| detailed_location | 86 | 100% | ||||
| health_condition_detail | 86 | 100% | 86 | |||
| latitude | 86 | 100% | 86 | |||
| location_region | 86 | 100% | 86 | |||
| longitude | 86 | 100% | 86 | |||
| timepoint_label | 86 | 100% | 86 | |||
| collection_date | 78 | 91% | 78 |
Archive description
This study focused on the gut virome of IBD patients
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.55. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “gut virome of IBD patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN21348987 | collection_date | 2018-10-11 | R1 | 0.90 | biosample.attribute:collection_date | 2018-10-11 |
| SAMN21348987 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:PA |
| SAMN21348987 | health_condition | ibd_unspecified | R1 | 0.85 | biosample.attribute:study_group | basic |
| SAMN21348987 | health_condition_detail | basic | R1 | 0.85 | biosample.attribute:study_group | basic |
| SAMN21348987 | latitude | 39.5700 | R1 | 0.90 | biosample.attribute:lat_lon | 39.57 N 75.13 W |
| SAMN21348987 | location_region | Pennsylvania | R1 | 0.75 | biosample.attribute:geo_loc_name | USA:PA |
| SAMN21348987 | longitude | -75.1300 | R1 | 0.90 | biosample.attribute:lat_lon | 39.57 N 75.13 W |
| SAMN21348987 | subject_id | 010 | R1 | 0.85 | sample.attr.subject_id | 010 |
| SAMN21348987 | timepoint_label | 01 | R1 | 0.70 | sample.name_rule:alias | 010-01 |
Sequencing
96 runs over 86 samples · mean 1.24 Gbp per run (median 1.38 Gbp, total 118.62 Gbp; 96 runs with a base count) · layout PAIRED 96 · platform ILLUMINA 96 · models NextSeq 550 (96) · 57% of runs with a Sandpiper profile · first public 2021-09-09
Authors (0)
No author record.
Downloads
PRJNA761454.csv.gz (3.5 KB) · parquet (74.6 KB) — all 86 samples, every field with route and confidence · PRJNA761454_determinations.csv.gz (6.6 KB) — 766 evidence rows