Gut microbiota in Crohn's disease patients, Moscow, Russia
Cross-sectional metagenomic study of 28 gut microbiota samples from Crohn's disease patients in Moscow, Russia, examining E. coli strain diversity and microbial community shifts associated with the disease. machine-written summary
28 samples · 28 runs · RU · Age unknown · 2015 · 1.77 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 196 sample values (collection date, country, latitude, location locality, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC6307143 |
| ✓ Supplementary tables | 56 sample values (age, sex) |
| ✓ External resources | 56 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
4 of 24 people sampled more than once (8 samples; median 2, up to 2 per person).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 28 | 100% | ||||
| country | 28 | 100% | 28 | |||
| health_condition | 28 | 100% | 28 | |||
| subject_id | 28 | 100% | 28 | |||
| age_at_collection_days | 28 | 100% | 28 | |||
| collection_date | 28 | 100% | 28 | |||
| detailed_location | 28 | 100% | ||||
| health_condition_detail | 28 | 100% | 28 | |||
| latitude | 28 | 100% | 28 | |||
| location_locality | 28 | 100% | 28 | |||
| location_region | 28 | 100% | 28 | |||
| longitude | 28 | 100% | 28 | |||
| sex | 28 | 100% | 28 |
- Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn's disease discovered using metagenomic and genomic analyses. 2018 PMID 30587114 PMC6307143 own_data
Archive description
Study of gut microbiota from patients with Crohn's disease
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.scientific_name · “human gut metagenome(28)”
- body site study.title · “Gut microbiota from patients with Crohn's disease”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN04113044 | age_at_collection_days | 14610.0 | R2 | 0.80 | paper.supp.12864_2018_5306_MOESM1_ESM.zip/Additional_Data.docx[table9!Age, years] | KI01: 40 |
| SAMN04113044 | collection_date | 2014 | R1 | 0.90 | biosample.attribute:collection_date | 2014 |
| SAMN04113044 | country | RU | R1 | 0.90 | sample.attr.geo_loc_name | Russia: Moscow |
| SAMN04113044 | health_condition | crohns_disease | R2 | 0.75 | external.gmrepo source | phenotype: Crohn Disease |
| SAMN04113044 | health_condition_detail | Crohn Disease | R2 | 0.75 | external.gmrepo source | phenotype: Crohn Disease |
| SAMN04113044 | latitude | 55.4500 | R1 | 0.90 | biosample.attribute:lat_lon | 55.45 N 37.37 E |
| SAMN04113044 | location_locality | Moscow | R1 | 0.85 | biosample.attribute:geo_loc_name | Russia: Moscow |
| SAMN04113044 | location_region | Moscow | R1 | 0.85 | biosample.attribute:geo_loc_name | Russia: Moscow |
| SAMN04113044 | longitude | 37.3700 | R1 | 0.90 | biosample.attribute:lat_lon | 55.45 N 37.37 E |
| SAMN04113044 | sex | female | R2 | 0.80 | paper.supp.12864_2018_5306_MOESM1_ESM.zip/Additional_Data.docx[table9!Sex] | KI01: F |
| SAMN04113044 | subject_id | KI01 | R1 | 0.70 | sample.name_rule:alias | KI01 |
Sequencing
28 runs over 28 samples · mean 1.84 Gbp per run (median 1.77 Gbp, total 51.45 Gbp; 28 runs with a base count) · layout SINGLE 28 · platform ABI_SOLID 22, ION_TORRENT 6 · models AB 5500 Genetic Analyzer (15), AB SOLiD 4 System (7), Ion Torrent PGM (6) · 0% of runs with a Sandpiper profile · first public 2015-10-02 – 2015-10-11
Authors (28)
Tyakht AV first · Manolov AI · Kanygina AV · Ischenko DS · Kovarsky BA · Popenko AS · Pavlenko AV · Elizarova AV · Rakitina DV · Baikova JP · Ladygina VG · Kostryukova ES · Karpova IY · Semashko TA · Larin AK · Grigoryeva TV · Sinyagina MN · Malanin SY · Shcherbakov PL · Kharitonova AY · Khalif IL · Shapina MV · Maev IV · Andreev DN · Belousova EA · Buzunova YM · Alexeev DG · Govorun VM last
Downloads
PRJNA296946.csv.gz (1.7 KB) · parquet (71.5 KB) — all 28 samples, every field with route and confidence · PRJNA296946_determinations.csv.gz (3.3 KB) — 308 evidence rows