Gut metagenomes in IBD vs healthy controls, Kazan, Russia
Case-control study of 3 gut metagenome samples from Kazan, Russia, comparing a healthy control, a Crohn's disease patient, and an ulcerative colitis patient. machine-written summary
100 samples · 105 runs · RU · Age unknown · 2023 · 4.08 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ✓ Abstract / description | 100 sample values (health condition detail) |
| ✓ Full text | 200 sample values (country, location site) · PMC10113391 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 3 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 | 100 | 100% | 100 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| detailed_location | 100 | 100% | ||||
| health_condition_detail | 100 | 100% | 100 | |||
| location_site | 100 | 100% | 100 |
- Results and lessons learned from the sbv IMPROVER metagenomics diagnostics for inflammatory bowel disease challenge. 2023 PMID 37072468 PMC10113391 own_data
Archive description
WGS gut metagenome of healthy individuals and IBD patients used for benchmarking MEDIC challenge
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SRR22050084 | country | RU | R3 | 0.70 | paper.fulltext.methods | individuals living in the republic of Tatarstan |
| SRR22050084 | health_condition_detail | mixed_case_control: Study includes both IBD patients (Ulcerative Colitis and Crohn's Disease) and non-IBD controls | R4 | 0.50 | paper.abstract | IBD and nonIBD subjects |
| SRR22050084 | location_site | Kazan Federal University | R3 | 0.70 | paper.fulltext.methods | ethics committee of the Kazan Federal University, Kazan, Russia |
Sequencing
105 runs over 100 samples · mean 4.14 Gbp per run (median 4.08 Gbp, total 434.95 Gbp; 105 runs with a base count) · layout PAIRED 105 · platform ILLUMINA 105 · models Illumina MiSeq (105) · 89% of runs with a Sandpiper profile · first public 2023-04-14
Authors (26)
Khachatryan L first · Xiang Y · Ivanov A · Glaab E · Graham G · Granata I · Giordano M · Maddalena L · Piccirillo M · Manipur I · Baruzzo G · Cappellato M · Avot B · Stan A · Battey J · Lo Sasso G · Boue S · Ivanov NV · Peitsch MC · Hoeng J · Falquet L · Di Camillo B · Guarracino MR · Ulyantsev V · Sierro N · Poussin C last
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJNA893901.csv.gz (3.1 KB) · parquet (72.8 KB) — all 100 samples, every field with route and confidence · PRJNA893901_determinations.csv.gz (1.9 KB) — 300 evidence rows