Colorectal cancer vs healthy mucosa microbiome, Gothenburg
20 samples from colorectal tissue in Gothenburg, Sweden, comparing tumoral and healthy mucosa (10 vs 10) using paired DNA and RNA deep-sequencing of bacterial and viral communities, case-control design. machine-written summary
20 samples · 20 runs · SE · Elderly · 2023 · 4.82 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 210 sample values (age, bmi, collection date, country, health condition, health condition detail, latitude, location locality) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10557870 |
| ○ 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 12 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 | 20 | 100% | ||||
| country | 20 | 100% | 20 | |||
| health_condition | 20 | 100% | 20 | |||
| subject_id | 20 | 100% | 20 | |||
| age_at_collection_days | 20 | 100% | 20 | |||
| collection_date | 20 | 100% | 20 | |||
| detailed_location | 20 | 100% | ||||
| health_condition_detail | 20 | 100% | 20 | |||
| latitude | 20 | 100% | 20 | |||
| location_locality | 20 | 100% | 20 | |||
| longitude | 20 | 100% | 20 | |||
| sex | 20 | 100% | 20 | |||
| bmi | 10 | 50% | 10 |
- Assessment of bacterial and viral gut communities in healthy and tumoral colorectal tissue using RNA and DNA deep sequencing. 2023 PMID 37641475 PMC10557870 own_data
Archive description
Assessment of bacterial and viral gut communities in healthy and tumoral colorectal mucosa using RNA and DNA deep-sequencing
How this project entered the registry
Classified as human blood / tissue / internal fluids / gut / stool shotgun DNA metagenome of elderly and adult by opus_adjudicated with confidence 0.45. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “healthy and tumoral colorectal mucosa”
- body site sample.attr.host_tissue_sampled · “colon (n=20/20)”
- life stage sample.attr.host_age · “68 (n=15/20)”
- life stage sample.attr.host_age · “67 (n=4/20)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN33730374 | age_at_collection_days | 27028.5 | R1 | 0.70 | sample.attr.host_age | 74 |
| SAMN33730374 | bmi | 23.6 | R1 | 0.90 | sample.attr.host_body_mass_index | 23.6 |
| SAMN33730374 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMN33730374 | country | SE | R1 | 0.90 | sample.attr.geo_loc_name | Sweden: Gothemburg |
| SAMN33730374 | health_condition | other_cancer | R1 | 0.85 | biosample_attr | cancer |
| SAMN33730374 | health_condition_detail | cancer | R1 | 0.90 | sample.attr.host_phenotype | cancer |
| SAMN33730374 | latitude | 57.7000 | R1 | 0.90 | biosample.attribute:lat_lon | 57.70 N 11.97 E |
| SAMN33730374 | location_locality | Gothenburg | R1 | 0.75 | biosample.attribute:geo_loc_name | Sweden: Gothemburg |
| SAMN33730374 | longitude | 11.9700 | R1 | 0.90 | biosample.attribute:lat_lon | 57.70 N 11.97 E |
| SAMN33730374 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN33730374 | subject_id | Patient 1 DNA | R1 | 0.85 | sample.attr.host_subject_id | Patient 1 DNA |
Sequencing
20 runs over 20 samples · mean 4.73 Gbp per run (median 4.82 Gbp, total 94.55 Gbp; 20 runs with a base count) · layout PAIRED 20 · platform ILLUMINA 20 · models Illumina NovaSeq 6000 (20) · 75% of runs with a Sandpiper profile · first public 2023-03-17
Authors (8)
Garcia-Serrano A first · Mukhedkar D · Hultin E · Rudsander U · Wettergren Y · Ure AE · Dillner J · Arroyo-Mühr LS last
Downloads
PRJNA943491.csv.gz (1.6 KB) · parquet (71.6 KB) — all 20 samples, every field with route and confidence · PRJNA943491_determinations.csv.gz (2.3 KB) — 210 evidence rows