Gut microbial autoantigen and colitis, Calgary, Canada
46 gut microbiome samples from Calgary, Canada, studying a gut microbial autoantigen linked to diabetogenic autoreactivity and colitis suppression; 6 samples labeled healthy controls; design otherwise unspecified. machine-written summary
23 samples · 46 runs · CA · Age unknown · 2017 · 3.27 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 227 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| – Abstract / description | no abstract or project description |
| – 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 37 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 | 23 | 100% | 23 | |||
| health_condition | 22 | 96% | 22 | |||
| subject_id | 22 | 96% | 22 | |||
| collection_date | 23 | 100% | 23 | |||
| detailed_location | 23 | 100% | ||||
| latitude | 23 | 100% | 23 | |||
| location_locality | 23 | 100% | 23 | |||
| location_region | 23 | 100% | 23 | |||
| longitude | 23 | 100% | 23 | |||
| sex | 23 | 100% | 23 | |||
| health_condition_detail | 22 | 96% | 22 |
- A Gut Microbial Mimic that Hijacks Diabetogenic Autoreactivity to Suppress Colitis. 2017 PMID 29053971 own_data
Archive description
A GUT MICROBIAL AUTOANTIGEN MIMIC THAT HIJACKS DIABETOGENIC AUTOREACTIVITY TO SUPPRESS COLITIS
How this project entered the registry
Classified as human and non-human (mixed) gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- host run.scientific_name · “mouse gut metagenome”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07490693 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMN07490693 | country | CA | R1 | 0.90 | sample.attr.geo_loc_name | Canada: Calgary |
| SAMN07490694 | health_condition | type1_diabetes | R1 | 0.70 | sample.name_rule:alias | T1D-1 |
| SAMN07490694 | health_condition_detail | T1D | R1 | 0.70 | sample.name_rule:alias | T1D-1 |
| SAMN07490693 | latitude | 51.0486 | R1 | 0.90 | biosample.attribute:lat_lon | 51.0486 N 114.0708 W |
| SAMN07490693 | location_locality | Calgary | R1 | 0.85 | biosample.attribute:geo_loc_name | Canada: Calgary |
| SAMN07490693 | location_region | Alberta | R1 | 0.60 | biosample.attribute:lat_lon | 51.0486 N 114.0708 W |
| SAMN07490693 | longitude | -114.0708 | R1 | 0.90 | biosample.attribute:lat_lon | 51.0486 N 114.0708 W |
| SAMN07490693 | sex | female | R1 | 0.85 | biosample.attribute:description | female |
| SAMN07490694 | subject_id | T1D subject 1 | R1 | 0.85 | biosample.attribute:source_material_id | T1D subject sample 1 |
Sequencing
46 runs over 23 samples · mean 3.45 Gbp per run (median 3.27 Gbp, total 158.77 Gbp; 46 runs with a base count) · layout PAIRED 46 · platform ILLUMINA 46 · models NextSeq 500 (46) · 80% of runs with a Sandpiper profile · first public 2017-08-11
Authors (0)
No author record.
Downloads
PRJNA397664.csv.gz (1.6 KB) · parquet (71.2 KB) — all 23 samples, every field with route and confidence · PRJNA397664_determinations.csv.gz (2.5 KB) — 227 evidence rows