Fecal metagenomes in gastric cancer vs chronic gastritis, Taiwan
65 fecal samples from adults and elderly patients in Taipei, Taiwan, comparing gut microbiome features between gastric cancer and chronic gastritis patients; case-control design. machine-written summary
65 samples · 65 runs · TW · Age unknown · 2024 · 7.12 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 650 sample values (age, collection date, country, health condition, health condition detail, latitude, location locality, location region) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 130 sample values (antibiotic exposure, subject id) · PMC11040827 |
| ○ 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 57 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 | 65 | 100% | ||||
| country | 65 | 100% | 65 | |||
| health_condition | 65 | 100% | 65 | |||
| subject_id | 65 | 100% | 65 | |||
| age_at_collection_days | 65 | 100% | 65 | |||
| antibiotic_exposure | 65 | 100% | 65 | |||
| collection_date | 65 | 100% | 65 | |||
| detailed_location | 65 | 100% | ||||
| health_condition_detail | 65 | 100% | 65 | |||
| latitude | 65 | 100% | 65 | |||
| location_locality | 65 | 100% | 65 | |||
| location_region | 65 | 100% | 65 | |||
| longitude | 65 | 100% | 65 | |||
| sex | 65 | 100% | 65 |
- Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study. 2024 PMID 38658841 PMC11040827 own_data
Archive description
To identify the differential abundance of gut microbiome features in the patients with gastric cancer compared to the patients with different stages of chronic gastritis.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “Gut microbiome associated with gastric cancer”
- life stage sample.attr.age · “47 (n=33/65)”
- life stage sample.attr.age · “70 (n=31/65)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN39472272 | age_at_collection_days | 19711.0 | R1 | 0.85 | sample.attr.age | 54 |
| SAMN39472272 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | intensive antibiotic treatments within 6 months before fecal sample collection |
| SAMN39472272 | collection_date | 2021-02-19 | R1 | 0.90 | biosample.attribute:collection_date | 2021-02-19 |
| SAMN39472272 | country | TW | R1 | 0.90 | sample.attr.geo_loc_name | Taiwan:Taipei |
| SAMN39472272 | health_condition | other_disease | R1 | 0.70 | sample.name_rule:class | gastritis_intestinalmetaplasia1 |
| SAMN39472272 | health_condition_detail | gastritis_intestinalmetaplasia | R1 | 0.70 | sample.name_rule:class | gastritis_intestinalmetaplasia1 |
| SAMN39472272 | latitude | 25.0330 | R1 | 0.90 | biosample.attribute:lat_lon | 25.0330 N 121.5654 E |
| SAMN39472272 | location_locality | Taipei | R1 | 0.85 | biosample.attribute:geo_loc_name | Taiwan:Taipei |
| SAMN39472272 | location_region | Taipei | R1 | 0.60 | biosample.attribute:lat_lon | 25.0330 N 121.5654 E |
| SAMN39472272 | longitude | 121.5654 | R1 | 0.90 | biosample.attribute:lat_lon | 25.0330 N 121.5654 E |
| SAMN39472272 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN39472272 | subject_id | SAMN39472272 | R3 | 0.75 | design.one_sample_per_subject:fulltext | the cross-sectional approach itself has limitations portraying only a snapshot of the time we collected the fecal samples |
Sequencing
65 runs over 65 samples · mean 7.55 Gbp per run (median 7.12 Gbp, total 490.76 Gbp; 65 runs with a base count) · layout PAIRED 65 · platform ILLUMINA 65 · models Illumina HiSeq 3000 (65) · 88% of runs with a Sandpiper profile · first public 2024-01-21
Authors (17)
Jeong S first · Liao YT · Tsai MH · Wang YK · Wu IC · Liu CJ · Wu MS · Chan TS · Chen MY · Hu PJ · Kao WY · Liu HC · Tsai MJ · Liu CY · Chang CC · Wu DC · Hsu YH last
Downloads
PRJNA1065874.csv.gz (3.1 KB) · parquet (74.7 KB) — all 65 samples, every field with route and confidence · PRJNA1065874_determinations.csv.gz (6.7 KB) — 780 evidence rows