IBD fecal metagenomes, Vercelli, Italy, cross-sectional
13 fecal metagenome samples from individuals with IBD in Vercelli, Italy, cross-sectional design, used as a disease-specificity control for CRC biomarkers in a larger study. machine-written summary
13 samples · 13 runs · IT · Age unknown · 2019 · 4.08 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 78 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ✓ Abstract / description | 26 sample values (health condition, health condition detail) |
| – 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 13 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 | 13 | 100% | 13 | |||
| health_condition | 13 | 100% | 13 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 13 | 100% | 13 | |||
| detailed_location | 13 | 100% | ||||
| health_condition_detail | 13 | 100% | 13 | |||
| latitude | 13 | 100% | 13 | |||
| location_locality | 13 | 100% | 13 | |||
| location_region | 13 | 100% | 13 | |||
| longitude | 13 | 100% | 13 |
Archive description
In the context of a larger whole-genome-shotgun metagenomic study about colorectal cancer (CRC), this set of samples served as an integration of the final validation of the discovered biomarkers: the rationale behind is collecting a moiety of samples related to a different disease with respect to the condition which constitute the main focus of the study, in order to use them to test the specificity of the biomarkers towards CRC.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.title · “Italian fecal metagenomes”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11153477 | collection_date | 2016-01-11 | R1 | 0.90 | biosample.attribute:collection_date | 2016-01-11 |
| SAMN11153477 | country | IT | R1 | 0.90 | sample.attr.geo_loc_name | Italy: Vercelli |
| SAMN11153477 | health_condition | ibd_unspecified | R4 | 0.50 | study.title | IBD Italian fecal metagenomes |
| SAMN11153477 | health_condition_detail | IBD (unspecified type); used as validation cohort for CRC biomarkers | R4 | 0.50 | study.title | IBD Italian fecal metagenomes |
| SAMN11153477 | latitude | 45.4140 | R1 | 0.90 | biosample.attribute:lat_lon | 45.414028 N 9.208268 E |
| SAMN11153477 | location_locality | Vercelli | R1 | 0.85 | biosample.attribute:geo_loc_name | Italy: Vercelli |
| SAMN11153477 | location_region | Lombardy | R1 | 0.60 | biosample.attribute:lat_lon | 45.414028 N 9.208268 E |
| SAMN11153477 | longitude | 9.2083 | R1 | 0.90 | biosample.attribute:lat_lon | 45.414028 N 9.208268 E |
Sequencing
13 runs over 13 samples · mean 4.69 Gbp per run (median 4.08 Gbp, total 61.02 Gbp; 13 runs with a base count) · layout PAIRED 13 · platform ILLUMINA 13 · models Illumina HiSeq 2000 (13) · 100% of runs with a Sandpiper profile · first public 2019-11-15
Authors (0)
No author record.
Downloads
PRJNA527369.csv.gz (1.3 KB) · parquet (70.5 KB) — all 13 samples, every field with route and confidence · PRJNA527369_determinations.csv.gz (1.2 KB) — 104 evidence rows