Gut metagenome in Crohn's disease, USA (PA)
40 gut metagenome samples from Pennsylvania, USA, including 23 healthy controls and 12 Crohn's disease cases. machine-written summary
40 samples · 40 runs · US · Age unknown · 2021 · 4.02 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 442 sample values (antibiotic exposure, collection date, country, health condition, health condition detail, intervention, intervention detail, latitude) |
| – 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 |
antibiotic exposure: two sequence archives disagree for 2 samples (e.g. no vs yes) — withheld.
The sources disagree on 2 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 (2)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN21353424 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN21353432 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
Genera, mean relative abundance over 4 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 | 40 | 100% | 40 | |||
| health_condition | 35 | 88% | 35 | |||
| subject_id | 40 | 100% | 40 | |||
| collection_date | 40 | 100% | 40 | |||
| detailed_location | 40 | 100% | ||||
| health_condition_detail | 40 | 100% | 40 | |||
| intervention | 40 | 100% | 40 | |||
| intervention_detail | 40 | 100% | 40 | |||
| latitude | 40 | 100% | 40 | |||
| location_region | 40 | 100% | 40 | |||
| longitude | 40 | 100% | 40 | |||
| antibiotic_exposure | 33 | 82% | 33 | |||
| medication | 7 | 18% | 7 | |||
| medication_detail | 7 | 18% | 7 |
Archive description
This study investigate the metagenome of the gut content after antimicrobial treatment
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 content after antimicrobial treatment”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN21353396 | antibiotic_exposure | no | R1 | 0.90 | biosample_attr | No |
| SAMN21353396 | collection_date | 2018-10-11 | R1 | 0.90 | biosample.attribute:collection_date | 2018-10-11 |
| SAMN21353396 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:PA |
| SAMN21353396 | health_condition | healthy_control | R1 | 0.90 | biosample_attr | Healthy |
| SAMN21353396 | health_condition_detail | Healthy | R1 | 0.90 | sample.attr.disease | Healthy |
| SAMN21353396 | intervention | antibiotic | R1 | 0.90 | biosample.attribute:study group | study group: Yes |
| SAMN21353396 | intervention_detail | assigned to antimicrobial treatment group | R1 | 0.90 | biosample.attribute:study group | study group: Yes |
| SAMN21353396 | latitude | 39.5700 | R1 | 0.90 | biosample.attribute:lat_lon | 39.57 N 75.13 W |
| SAMN21353396 | location_region | Pennsylvania | R1 | 0.75 | biosample.attribute:geo_loc_name | USA:PA |
| SAMN21353396 | longitude | -75.1300 | R1 | 0.90 | biosample.attribute:lat_lon | 39.57 N 75.13 W |
| SAMN21353424 | medication | corticosteroid;immunosuppressant_or_biologic | R1 | 0.85 | biosample.attribute:other_immunosuppression | prednisone |
| SAMN21353424 | medication_detail | prednisone | R1 | 0.85 | biosample.attribute:other_immunosuppression | prednisone |
| SAMN21353396 | subject_id | A2 | R1 | 0.85 | sample.attr.subject_id | A2 |
Sequencing
40 runs over 40 samples · mean 4.17 Gbp per run (median 4.02 Gbp, total 166.68 Gbp; 40 runs with a base count) · layout PAIRED 40 · platform ILLUMINA 40 · models Illumina HiSeq 2500 (40) · 15% of runs with a Sandpiper profile · first public 2021-09-09
Authors (0)
No author record.
Downloads
PRJNA761533.csv.gz (2.4 KB) · parquet (73.0 KB) — all 40 samples, every field with route and confidence · PRJNA761533_determinations.csv.gz (4.1 KB) — 442 evidence rows