Gut microbiome in stage III colorectal cancer, Mali
Shotgun metagenome study of 46 gut microbiome samples from Mali, comparing 22 samples from stage III colorectal cancer patients and 24 from healthy controls, using a case-control design. machine-written summary
46 samples · 46 runs · ML · Age unknown · 2023 · 6.84 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 276 sample values (collection date, country, health condition, health condition detail, latitude, longitude) |
| ✓ Abstract / description | 46 sample values (subject id) |
| – Full text | no open-access full text linked |
| – 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 42 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 | 0 | 0% | ||||
| country | 46 | 100% | 46 | |||
| health_condition | 46 | 100% | 46 | |||
| subject_id | 46 | 100% | 46 | |||
| collection_date | 46 | 100% | 46 | |||
| health_condition_detail | 46 | 100% | 46 | |||
| latitude | 46 | 100% | 46 | |||
| longitude | 46 | 100% | 46 |
- Characterization of the gut microbiota in patients with stage III colorectal cancer: A case-control study. 2026 PMID 41270896 own_data
Archive description
we used shotgun metagenome sequencing to characterize the gut microbiome in advanced stage of CRC through a case control study in Mali.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “gut microbiota in patients with stage III colorectal cancer”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN33356256 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMN33356256 | country | ML | R1 | 0.90 | sample.attr.geo_loc_name | Mali |
| SAMN33356256 | health_condition | colorectal_cancer | R1 | 0.70 | sample.name_rule:description | description: CRC |
| SAMN33356256 | health_condition_detail | CRC (stage III colorectal cancer case) | R1 | 0.70 | sample.name_rule:description | description: CRC |
| SAMN33356256 | latitude | 17.5700 | R1 | 0.90 | biosample.attribute:lat_lon | 17.57 N 3.99 W |
| SAMN33356256 | longitude | -3.9900 | R1 | 0.90 | biosample.attribute:lat_lon | 17.57 N 3.99 W |
| SAMN33356256 | subject_id | SAMN33356256 | R4 | 0.65 | design.one_sample_per_subject:abstract | This case-control study involved newly diagnosed CRC patients (n = 23) prior to any treatment initiation, and unrelated healthy controls (n = 24) |
Sequencing
46 runs over 46 samples · mean 6.69 Gbp per run (median 6.84 Gbp, total 307.78 Gbp; 46 runs with a base count) · layout PAIRED 46 · platform ILLUMINA 46 · models Illumina HiSeq 4000 (46) · 91% of runs with a Sandpiper profile · first public 2023-02-27
Authors (0)
No author record.
Downloads
PRJNA936589.csv.gz (2.1 KB) · parquet (71.4 KB) — all 46 samples, every field with route and confidence · PRJNA936589_determinations.csv.gz (3.0 KB) — 322 evidence rows