Colon cancer mucosal microbiome, Nanning China, case-control
38 tumor and adjacent non-cancerous mucosal samples from colon cancer patients in Nanning, China, analyzed by metagenomic sequencing to characterize mucosal microbiota composition in a case-control design. machine-written summary
38 samples · 38 runs · CN · Adult · 2023 · 6.75 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 190 sample values (age, collection date, country, location locality, sex) |
| ✓ Abstract / description | 76 sample values (health condition, health condition detail) |
| ✓ Full text | 76 sample values (antibiotic exposure, location site) · PMC11915798 |
| ✓ Supplementary tables | 38 sample values (subject id) |
| – 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 |
longitudinal — not resolved
19 of 19 people sampled more than once (38 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 28 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 | 38 | 100% | ||||
| country | 38 | 100% | 38 | |||
| health_condition | 38 | 100% | 38 | |||
| subject_id | 38 | 100% | 38 | |||
| age_at_collection_days | 38 | 100% | 38 | |||
| antibiotic_exposure | 38 | 100% | 38 | |||
| collection_date | 38 | 100% | 38 | |||
| detailed_location | 38 | 100% | ||||
| health_condition_detail | 38 | 100% | 38 | |||
| location_locality | 38 | 100% | 38 | |||
| location_site | 38 | 100% | 38 | |||
| sex | 38 | 100% | 38 |
- Multi-omics analysis reveals associations between gut microbiota and host transcriptome in colon cancer patients. 2025 PMID 40013792 PMC11915798 own_data
Archive description
To investigate the role of intestinal mucosal microbiota in colon cancer, we colected tumor and adiacentnon-cancerous mucosal samples from colon cancer patients for Metagenomics sequencing to further elucidate the functional composition of colon cancer mucosal microbiota.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “intestinal mucosal microbiota in colon cancer”
- life stage sample.attr.age · “34 (n=24/38)”
- life stage sample.attr.age · “62 (n=14/38)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN37813977 | age_at_collection_days | 23741.2 | R1 | 0.70 | sample.attr.age | 65 |
| SAMN37813977 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | not undergone any antibiotic therapy within the past month |
| SAMN37813977 | collection_date | 2022-01 | R1 | 0.90 | biosample.attribute:collection_date | 2022-01 |
| SAMN37813977 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China: Nanning |
| SAMN37813977 | health_condition | colorectal_cancer | R4 | 0.50 | paper.abstract | collected mucosal and tissue samples from both the tumor and normal regions |
| SAMN37813977 | health_condition_detail | colon cancer with tumor and normal mucosal samples | R4 | 0.50 | paper.abstract | colon cancer patients |
| SAMN37813977 | location_locality | Nanning | R1 | 0.85 | biosample.attribute:geo_loc_name | China: Nanning |
| SAMN37813977 | location_site | Cancer Hospital Affiliated to Guangxi Medical University | R3 | 0.70 | paper.fulltext.methods | Cancer Hospital Affiliated to Guangxi Medical University |
| SAMN37813977 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN37813977 | subject_id | 1 | R2 | 0.85 | paper.supp.msystems.00805-24-s0002.xlsx[Table S1!Patient ID] | 1 |
Sequencing
38 runs over 38 samples · mean 6.64 Gbp per run (median 6.75 Gbp, total 252.45 Gbp; 38 runs with a base count) · layout PAIRED 38 · platform ILLUMINA 38 · models Illumina NovaSeq 6000 (38) · 92% of runs with a Sandpiper profile · first public 2023-10-16
Authors (11)
Qin Y first · Wang Q · Lin Q · Liu F · Pan X · Wei C · Chen J · Huang T · Fang M · Yang W · Pan L last
Downloads
PRJNA1028158.csv.gz (2.1 KB) · parquet (72.4 KB) — all 38 samples, every field with route and confidence · PRJNA1028158_determinations.csv.gz (3.7 KB) — 380 evidence rows