Viral metagenome of children's stool samples, Ethiopia
29 stool samples from healthy children in Amhara, Ethiopia, analyzed by viral metagenomics; curated records indicate an intervention-based study design. machine-written summary
29 samples · 29 runs · ET · Child · 2017 · 0.14 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 145 sample values (collection date, country, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 58 sample values (lifestyle, lifestyle detail) · PMC6095524, PMC6832430 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 58 sample values (health condition, health condition detail) · from African Human Microbiome Portal (H3ABioNet) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Other administered intervention (see intervention_detail) design observational_with_procedure · population healthy_control · New hand-dug water well (clean water intervention)
“clean water intervention trial” — abstract:30114205 (study level; per-sample arms are in the intervention column below)
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 | 29 | 100% | ||||
| country | 29 | 100% | 29 | |||
| health_condition | 29 | 100% | 29 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 29 | 100% | 29 | |||
| detailed_location | 29 | 100% | ||||
| health_condition_detail | 29 | 100% | 29 | |||
| latitude | 29 | 100% | 29 | |||
| lifestyle | 29 | 100% | 29 | |||
| lifestyle_detail | 29 | 100% | 29 | |||
| location_region | 29 | 100% | 29 | |||
| longitude | 29 | 100% | 29 |
- Enteric virome of Ethiopian children participating in a clean water intervention trial. 2018 PMID 30114205 PMC6095524 own_data
- Viruses in Horses with Neurologic and Respiratory Diseases. 2019 PMID 31614994 PMC6832430 own_data
Archive description
Viral metagenome of children stool sample from Ethiopia
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by deterministic_rule with confidence 0.90. Assay shotgun_dna.
- host run.host_tax_id · “host_tax_id 9606”
- body site study.title · “metagenome of children stool sample from Ethiopia”
- body site study.description · “metagenome of children stool sample from Ethiopia”
- life stage study.title · “Viral metagenome of children stool sample from”
- life stage study.description · “Viral metagenome of children stool sample from”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07818838 | collection_date | 2016-04-01 | R1 | 0.90 | biosample.attribute:collection_date | 2016-04-01 |
| SAMN07818838 | country | ET | R1 | 0.90 | sample.attr.geo_loc_name | Ethiopia: Amhara |
| SAMN07818838 | health_condition | healthy_control | R2 | 0.70 | external.ahmp source | DISEASE: Healthy |
| SAMN07818838 | health_condition_detail | Healthy | R2 | 0.70 | external.ahmp source | DISEASE: Healthy |
| SAMN07818838 | latitude | 11.3900 | R1 | 0.90 | biosample.attribute:lat_lon | 11.39 N 37.57 E |
| SAMN07818838 | lifestyle | rural_non_industrialized | R3 | 0.70 | paper.fulltext.methods | rural agrarian region in the Goncha Siso Enese district |
| SAMN07818838 | lifestyle_detail | rural agrarian children, Amhara Ethiopia | R3 | 0.70 | paper.fulltext.methods | rural agrarian region in the Goncha Siso Enese district |
| SAMN07818838 | location_region | Amhara | R1 | 0.85 | biosample.attribute:geo_loc_name | Ethiopia: Amhara |
| SAMN07818838 | longitude | 37.5700 | R1 | 0.90 | biosample.attribute:lat_lon | 11.39 N 37.57 E |
Sequencing
29 runs over 29 samples · mean 0.17 Gbp per run (median 0.14 Gbp, total 4.92 Gbp; 29 runs with a base count) · layout PAIRED 29 · platform ILLUMINA 29 · models Illumina MiSeq (29) · 69% of runs with a Sandpiper profile · first public 2017-10-21
Authors (14)
Altan E first · Aiemjoy K · Phan TG · Deng X · Aragie S · Tadesse Z · Callahan KE · Keenan J · Delwart E last · Li Y · Sabino-Santos G · Sawaswong V · Barnum S · Pusterla N
Downloads
PRJNA415207.csv.gz (1.6 KB) · parquet (71.1 KB) — all 29 samples, every field with route and confidence · PRJNA415207_determinations.csv.gz (2.6 KB) — 261 evidence rows