Human gut phageome protocol development, 84 adult samples
84 faecal samples from adults, used to develop and test a reproducible viral metagenome extraction protocol, examining effects of storage conditions, freeze-thaw cycles, operator bias, and phage spiking on phageome profiles. machine-written summary
84 samples · 84 runs · Age unknown · 2018 · 2.12 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 116 sample values (subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 84 sample values (location region) · PMC5892011, PMC8103869 |
| ✓ Supplementary tables | 139 sample values (age, sex) |
| – 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 |
intervention — arms not resolved
design observational_with_procedure · Exogenous phage spiking of faecal samples for quantification
longitudinal — not resolved
13 of 16 people sampled more than once (78 samples; median 6, up to 9 per person). Schedule stated by the source: “Same individuals sampled repeatedly across storage/freeze-thaw experiments; timepoints labeled T0,T1,T3,T5,T6,T17,T24; also 6h and 24h room-temp timepoints; 5 consecutive daily freeze-thaw cycles”.
Genera, mean relative abundance over 63 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 | 84 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 0 | 0% | ||||
| subject_id | 81 | 96% | 81 | |||
| detailed_location | 84 | 100% | ||||
| location_region | 84 | 100% | 84 | |||
| sex | 77 | 92% | 77 | |||
| age_at_collection_days | 62 | 74% | 62 | |||
| timepoint_label | 35 | 42% | 35 |
- Reproducible protocols for metagenomic analysis of human faecal phageomes. 2018 PMID 29631623 PMC5892011 own_data
- Rengasvirus, a Circular Replication-Associated Protein-Encoding Single-Stranded DNA Virus-Related Genome That Is a Common Contaminant in Metagenomic Data. 2021 PMID 33958399 PMC8103869 unsure
Archive description
Study of factors impacting viral metagenome analysis
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site sample.attr.isolation_source · “feces filtered for virus-like particles (n=84/84)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07646474 | age_at_collection_days | 16436 | R2 | 0.85 | paper.supp.40168_2018_446_MOESM2_ESM.xlsx[Table S2!Age] | 45 |
| SAMN07646474 | location_region | Cork | R3 | 0.70 | paper.fulltext.methods | approved by the Cork Research Ethics Committee |
| SAMN07646474 | sex | female | R2 | 0.85 | paper.supp.40168_2018_446_MOESM2_ESM.xlsx[Table S2!Gender] | F |
| SAMN07646474 | subject_id | 925 | R1 | 0.70 | sample.name_rule:TITLE | Spk_925_10_0 |
| SAMN07646487 | timepoint_label | T0 | R1 | 0.70 | sample.name_rule:TITLE | APF1_T0 |
Sequencing
84 runs over 84 samples · mean 2.21 Gbp per run (median 2.12 Gbp, total 185.84 Gbp; 84 runs with a base count) · layout PAIRED 84 · platform ILLUMINA 84 · models Illumina MiSeq (84) · 75% of runs with a Sandpiper profile · first public 2018-05-03
Authors (30)
Shkoporov AN first · Ryan FJ · Draper LA · Forde A · Stockdale SR · Daly KM · McDonnell SA · Nolan JA · Sutton TDS · Dalmasso M · McCann A · Ross RP · Hill C last · Keeler EL first · Taylor LJ · Abbas A · Collman RG · Bushman FD last · Zeng S first · Almeida A · Li S · Ying J · Wang H · Qu Y · Paul Ross R · Stanton C · Zhou Z · Niu X · Mu D · Wang S last
Help complete this project
2 of the 4 core fields are below 50% coverage: country, health_condition. Share metadata
Downloads
PRJNA407341.csv.gz (2.9 KB) · parquet (72.7 KB) — all 84 samples, every field with route and confidence · PRJNA407341_determinations.csv.gz (3.2 KB) — 339 evidence rows