Gastric Mucosa Phageome in Adults, Wrocław, Poland
103 stomach biopsy samples from adult and elderly patients with other disease in Wrocław, Poland, analyzed for phage sequences in a cross-sectional design. machine-written summary
103 samples · 103 runs · PL · Age unknown · 2023 · 1.20 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 921 sample values (age, collection date, country, latitude, location locality, location region, longitude, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 206 sample values (health condition, health condition detail) · PMC10417112 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 |
Genera, mean relative abundance over 41 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 | 103 | 100% | ||||
| country | 103 | 100% | 103 | |||
| health_condition | 103 | 100% | 103 | |||
| subject_id | 103 | 100% | 103 | |||
| detailed_location | 103 | 100% | ||||
| health_condition_detail | 103 | 100% | 103 | |||
| latitude | 103 | 100% | 103 | |||
| location_locality | 103 | 100% | 103 | |||
| location_region | 103 | 100% | 103 | |||
| longitude | 103 | 100% | 103 | |||
| age_at_collection_days | 101 | 98% | 101 | |||
| collection_date | 101 | 98% | 101 | |||
| sex | 101 | 98% | 101 |
- New Phage-Derived Antibacterial Enzyme PolaR Targeting Rothia spp. 2023 PMID 37566076 PMC10417112 own_data
Archive description
Phageomes derived from tissue sections taken from the human stomach
How this project entered the registry
Classified as human other human site / gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.title · “Phageomes from human stomach”
- body site study.description · “tissue sections taken from the human stomach”
- body site sample.attr.isolation_source · “stomach (n=103/103)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN33273702 | age_at_collection_days | 10957.5 | R1 | 0.85 | sample.attr.gender_and_age | Male_30 |
| SAMN33273702 | collection_date | 2018-01-30 | R1 | 0.90 | biosample.attribute:collection_date | 2018-01-30 |
| SAMN33273702 | country | PL | R1 | 0.90 | sample.attr.geo_loc_name | Poland:Wroclaw |
| SAMN33273702 | health_condition | other_disease | R3 | 0.60 | paper.fulltext.results | patients affected by gastric disorders |
| SAMN33273702 | health_condition_detail | patients affected by gastric disorders | R3 | 0.60 | paper.fulltext.results | patients affected by gastric disorders |
| SAMN33273702 | latitude | 51.1100 | R1 | 0.90 | biosample.attribute:lat_lon | 51.11 N 17.03 E |
| SAMN33273702 | location_locality | Wrocław | R1 | 0.75 | biosample.attribute:geo_loc_name | Poland:Wroclaw |
| SAMN33273702 | location_region | Lower Silesian Voivodeship | R1 | 0.60 | biosample.attribute:lat_lon | 51.11 N 17.03 E |
| SAMN33273702 | longitude | 17.0300 | R1 | 0.90 | biosample.attribute:lat_lon | 51.11 N 17.03 E |
| SAMN33273702 | sex | male | R1 | 0.90 | sample.attr.gender_and_age | Male_30 |
| SAMN33273702 | subject_id | Patient no 1 | R1 | 0.85 | biosample.attribute:source_material_id | Patient no 1 |
Sequencing
103 runs over 103 samples · mean 1.32 Gbp per run (median 1.20 Gbp, total 136.33 Gbp; 103 runs with a base count) · layout PAIRED 103 · platform ILLUMINA 103 · models NextSeq 550 (103) · 50% of runs with a Sandpiper profile · first public 2023-02-27 – 2023-06-24
Authors (15)
Miernikiewicz P first · Barylski J · Wilczak A · Dragoš A · Rybicka I · Bałdysz S · Szymczak A · Dogsa I · Rokush K · Harhala MA · Ciekot J · Ferenc S · Gnus J · Witkiewicz W · Dąbrowska K last
Downloads
PRJNA934363.csv.gz (4.4 KB) · parquet (76.4 KB) — all 103 samples, every field with route and confidence · PRJNA934363_determinations.csv.gz (9.9 KB) — 1,127 evidence rows