Gut microbiome/resistome in CRC, biopsy vs lavage, Guangdong
40 samples (paired biopsy tissue and intestinal lavage fluid from 20 colorectal cancer patients) from Guangdong, China, analyzed by shotgun metagenomics in a case-control design comparing microbiomes and antibiotic resistance genes between sample types. machine-written summary
40 samples · 40 runs · CN · Adult · 2023 · 7.08 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 160 sample values (collection date, country, location region, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 120 sample values (antibiotic exposure, health condition, health condition detail, location site) · PMC8484797 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 40 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – 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 19 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 | 40 | 100% | ||||
| country | 40 | 100% | 40 | |||
| health_condition | 40 | 100% | 20 | 20 | ||
| subject_id | 40 | 100% | 40 | |||
| antibiotic_exposure | 40 | 100% | 40 | |||
| collection_date | 40 | 100% | 40 | |||
| detailed_location | 40 | 100% | ||||
| health_condition_detail | 40 | 100% | 20 | 20 | ||
| location_region | 40 | 100% | 40 | |||
| location_site | 40 | 100% | 40 |
- Microbiomes and Resistomes in Biopsy Tissue and Intestinal Lavage Fluid of Colorectal Cancer. 2021 PMID 34604238 PMC8484797 own_data
Archive description
Microbiomes and resistomes in biopsy tissue and intestinal lavage fluid of colorectal cancer
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.description · “biopsy tissue and intestinal lavage fluid of”
- body site external_curation.infant_catalog · “body_site_call gut”
- body site study.description · “and resistomes in biopsy tissue and intestinal”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN20792634 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | None of the patients received antibiotics before sample collection |
| SAMN20792634 | collection_date | 2019-04-04 | R1 | 0.90 | biosample.attribute:collection_date | 2019-04-04 |
| SAMN20792634 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China: Guangdong |
| SAMN20792654 | health_condition | colorectal_cancer | R2 | 0.75 | external.gmrepo source | phenotype: Colorectal Neoplasms |
| SAMN20792634 | health_condition | colorectal_cancer | R3 | 0.70 | paper.fulltext.methods | Pathological tests diagnosed 20 CRC patients |
| SAMN20792654 | health_condition_detail | Colorectal Neoplasms | R2 | 0.75 | external.gmrepo source | phenotype: Colorectal Neoplasms |
| SAMN20792634 | health_condition_detail | newly diagnosed CRC patients | R3 | 0.70 | paper.fulltext.methods | Pathological tests diagnosed 20 CRC patients |
| SAMN20792634 | location_region | Guangdong | R1 | 0.85 | biosample.attribute:geo_loc_name | China: Guangdong |
| SAMN20792634 | location_site | Second Affiliated Hospital of Shantou University | R3 | 0.70 | paper.fulltext.methods | selected from the Second Affiliated Hospital of Shantou University |
| SAMN20792634 | subject_id | 1 | R1 | 0.70 | sample.name_rule:alias | Tissue1 |
Sequencing
40 runs over 40 samples · mean 7.05 Gbp per run (median 7.08 Gbp, total 282.03 Gbp; 40 runs with a base count) · layout PAIRED 40 · platform ILLUMINA 40 · models Illumina NovaSeq 6000 (40) · 85% of runs with a Sandpiper profile · first public 2023-08-18
Downloads
PRJNA754518.csv.gz (2.1 KB) · parquet (71.7 KB) — all 40 samples, every field with route and confidence · PRJNA754518_determinations.csv.gz (3.5 KB) — 320 evidence rows