Stool metagenomics in CRC and healthy controls, Turkey
Case-control study of 71 stool shotgun metagenomic samples from Turkey, comparing colorectal cancer patients (32) and healthy controls (39). machine-written summary
71 samples · 71 runs · TR · Age unknown · 2024 · 12.53 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 497 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12283368 |
| ✓ Supplementary tables | 91 sample values (bmi, 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
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 | 0 | 0% | ||||
| country | 71 | 100% | 71 | |||
| health_condition | 71 | 100% | 71 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 71 | 100% | 71 | |||
| detailed_location | 71 | 100% | ||||
| health_condition_detail | 71 | 100% | 71 | |||
| latitude | 71 | 100% | 71 | |||
| location_region | 71 | 100% | 71 | |||
| longitude | 71 | 100% | 71 | |||
| sex | 57 | 80% | 57 | |||
| bmi | 34 | 48% | 34 |
- Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer. 2025 PMID 40461820 PMC12283368 unsure
Archive description
The dataset contains stool shotgun metagenomic sequencing data of a cohort of Turkish CRC patients and healthy controls. Human reads were removed before the submission.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “Human reads were removed before the submission”
- body site study.description · “stool shotgun metagenomic sequencing data”
- body site run.scientific_name · “gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN44019346 | bmi | 23.1 | R2 | 0.85 | paper.supp.41591_2025_3693_MOESM2_ESM.xlsx[Table 2!BMI] | 23.1 |
| SAMN44019343 | collection_date | 2021-01-27 | R1 | 0.90 | biosample.attribute:collection_date | 2021-01-27 |
| SAMN44019343 | country | TR | R1 | 0.90 | sample.attr.geo_loc_name | Turkey |
| SAMN44019343 | health_condition | colorectal_cancer | R1 | 0.70 | sample.name_rule:title | H1_1 CRC - Stool metagenomics |
| SAMN44019343 | health_condition_detail | CRC | R1 | 0.70 | sample.name_rule:title | H1_1 CRC - Stool metagenomics |
| SAMN44019343 | latitude | 40.9722 | R1 | 0.90 | biosample.attribute:lat_lon | 40.972200 N 29.152200 E |
| SAMN44019343 | location_region | Istanbul | R1 | 0.60 | biosample.attribute:lat_lon | 40.972200 N 29.152200 E |
| SAMN44019343 | longitude | 29.1522 | R1 | 0.90 | biosample.attribute:lat_lon | 40.972200 N 29.152200 E |
| SAMN44019345 | sex | male | R2 | 0.85 | paper.supp.41591_2025_3693_MOESM2_ESM.xlsx[Table 2!Sex] | male |
Sequencing
71 runs over 71 samples · mean 12.35 Gbp per run (median 12.53 Gbp, total 877.04 Gbp; 71 runs with a base count) · layout PAIRED 71 · platform ILLUMINA 71 · models Illumina NovaSeq 6000 (71) · 89% of runs with a Sandpiper profile · first public 2024-10-03
Authors (40)
Piccinno G first · Thompson KN · Manghi P · Ghazi AR · Thomas AM · Blanco-Míguez A · Asnicar F · Mladenovic K · Pinto F · Armanini F · Punčochář M · Piperni E · Heidrich V · Fackelmann G · Ferrero G · Tarallo S · Nguyen LH · Yan Y · Keles NA · Tuna BG · Vymetalkova V · Trompetto M · Liska V · Hucl T · Vodicka P · Bencsiková B · Čarnogurská M · Popovici V · Marmorino F · Cremolini C · Pardini B · Cordero F · Song M · Chan AT · Derosa L · Zitvogel L · Huttenhower C · Naccarati A · Budinska E · Segata N last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJNA1167935.csv.gz (3.1 KB) · parquet (73.7 KB) — all 71 samples, every field with route and confidence · PRJNA1167935_determinations.csv.gz (5.0 KB) — 588 evidence rows