Fecal virome, Venezuelan children, uncontacted vs connected
Cross-sectional study of 80 fecal samples from children (neonate, infant, child) in Venezuela, comparing uncontacted Amerindian populations with a more connected village and Caracas. machine-written summary
80 samples · 80 runs · VE · Child · 2018 · 0.12 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 320 sample values (age, collection date, country, sex) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC8095712 |
| – 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 80 | 100% | ||||
| country | 80 | 100% | 80 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 80 | 100% | 80 | |||
| collection_date | 80 | 100% | 80 | |||
| sex | 80 | 100% | 80 |
- Inter-Individual Diversity Scaling Analysis of the Human Virome With Classic Diversity-Area Relationship (DAR) Modeling. 2021 PMID 33959147 PMC8095712 unsure
Archive description
The aim of the study was to analyzed the fecal virome of children in two small uncontacted populations and compare them to those of age-matched children from a more connected Venezuelan village and the city of Caracas.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child and neonate and infant / toddler and adult by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “fecal virome”
- life stage study.description · “virome of children in two”
- life stage sample.attr.host_age · “0 (n=14/80)”
- life stage sample.attr.host_age · “2 (n=12/80)”
- life stage sample.attr.host_age · “1 (n=11/80)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN08013693 | age_at_collection_days | 730.0 | R1 | 0.85 | sample.attr.host_age | 2 |
| SAMN08013693 | collection_date | 2015 | R1 | 0.90 | biosample.attribute:collection_date | 2015 |
| SAMN08013693 | country | VE | R1 | 0.90 | sample.attr.geo_loc_name | Venezuela |
| SAMN08013693 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
Sequencing
80 runs over 80 samples · mean 0.16 Gbp per run (median 0.12 Gbp, total 12.98 Gbp; 80 runs with a base count) · layout PAIRED 80 · platform ILLUMINA 80 · models Illumina MiSeq (80) · 0% of runs with a Sandpiper profile · first public 2018-01-31
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA418044.csv.gz (2.8 KB) · parquet (72.5 KB) — all 80 samples, every field with route and confidence · PRJNA418044_determinations.csv.gz (2.0 KB) — 320 evidence rows