Gut metagenomes, colorectal cancer vs healthy, Minnesota
Cross-sectional study of 4 stool metagenome samples from adults (3) and an elderly subject (1) in Rochester, Minnesota, comparing colorectal cancer (2) and healthy control (2) samples to reconstruct gut microbial genomes. machine-written summary
4 samples · 16 runs · US · Adult · 2016 · 358.16 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 44 sample values (age, bmi, collection date, country, health condition, health condition detail, latitude, location locality) |
| ✓ Abstract / description | 4 sample values (health condition, health condition detail) |
| ✓ Full text | 4 sample values (location site) · PMC4880562 |
| ○ 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 4 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 | 4 | 100% | ||||
| country | 4 | 100% | 4 | |||
| health_condition | 4 | 100% | 2 | 2 | ||
| subject_id | 4 | 100% | 4 | |||
| age_at_collection_days | 4 | 100% | 4 | |||
| bmi | 4 | 100% | 4 | |||
| collection_date | 4 | 100% | 4 | |||
| detailed_location | 4 | 100% | ||||
| health_condition_detail | 4 | 100% | 2 | 2 | ||
| latitude | 4 | 100% | 4 | |||
| location_locality | 4 | 100% | 4 | |||
| location_region | 4 | 100% | 4 | |||
| location_site | 4 | 100% | 4 | |||
| longitude | 4 | 100% | 4 | |||
| sex | 4 | 100% | 4 |
- Capturing One of the Human Gut Microbiome's Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data. 2016 PMID 27303377 PMC4880562 own_data
Archive description
We aim to reconstruct genomes from metagenomic sequences based on multiple sequencing strategies, for characterization of organisms present in the human gut environment.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “Genome reconstructions from human gut metagenomes”
- life stage sample.attr.host_age · “51 (n=3/4)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN04523137 | age_at_collection_days | 30702.0 | R1 | 0.85 | sample.attr.host_age | 84 |
| SAMN04523137 | bmi | 25.32 | R1 | 0.90 | sample.attr.host_body_mass_index | 25.32 |
| SAMN04523137 | collection_date | 2002-05 | R1 | 0.90 | biosample.attribute:collection_date | 2002-05 |
| SAMN04523137 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:Minnesota,Rochester |
| SAMN04523137 | health_condition | colorectal_cancer | R1 | 0.70 | biosample_attr | Colorectal Cancer, Stage I |
| SAMN04523139 | health_condition | healthy_control | R4 | 0.50 | paper.abstract | healthy volunteers |
| SAMN04523137 | health_condition_detail | Colorectal Cancer, Stage I | R1 | 0.90 | sample.attr.host_disease | Colorectal Cancer, Stage I |
| SAMN04523139 | health_condition_detail | Healthy volunteers | R4 | 0.50 | paper.abstract | healthy volunteers |
| SAMN04523137 | latitude | 44.0234 | R1 | 0.90 | biosample.attribute:lat_lon | 44.0234 N 92.46295 W |
| SAMN04523137 | location_locality | Rochester | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Minnesota,Rochester |
| SAMN04523137 | location_region | Minnesota | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Minnesota,Rochester |
| SAMN04523137 | location_site | Mayo Clinic | R3 | 0.70 | paper.fulltext.methods | patients at the Mayo Clinic |
| SAMN04523137 | longitude | -92.4630 | R1 | 0.90 | biosample.attribute:lat_lon | 44.0234 N 92.46295 W |
| SAMN04523137 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN04523137 | subject_id | A254 | R1 | 0.85 | sample.attr.host_subject_id | A254 |
Sequencing
16 runs over 4 samples · mean 84.83 Gbp per run (median 91.46 Gbp, total 1,357.26 Gbp; 16 runs with a base count) · layout PAIRED 16 · platform ILLUMINA 16 · models Illumina HiSeq 2500 (16) · 56% of runs with a Sandpiper profile · first public 2016-04-20
Authors (10)
Jeraldo P first · Hernandez A · Nielsen HB · Chen X · White BA · Goldenfeld N · Nelson H · Alhquist D · Boardman L · Chia N last
Downloads
PRJNA312222.csv.gz (1.2 KB) · parquet (71.3 KB) — all 4 samples, every field with route and confidence · PRJNA312222_determinations.csv.gz (1.4 KB) — 52 evidence rows