Gut metagenomes in alcohol dependence and cirrhosis, Russia
99 stool shotgun metagenome samples from adult patients in Russia with alcohol dependence syndrome, with and without alcoholic liver cirrhosis, compared to an external control group in a case-control design. machine-written summary
99 samples · 99 runs · RU · Adult · 2016 · 1.06 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 457 sample values (collection date, country, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 198 sample values (antibiotic exposure, subject id) · PMC5257029, PMC5645934 |
| ✓ Supplementary tables | 484 sample values (age, bmi, health condition, health condition detail, sex) |
| – 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 |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 99 | 100% | ||||
| country | 99 | 100% | 99 | |||
| health_condition | 99 | 100% | 99 | |||
| subject_id | 99 | 100% | 99 | |||
| antibiotic_exposure | 99 | 100% | 99 | |||
| collection_date | 99 | 100% | 99 | |||
| health_condition_detail | 99 | 100% | 99 | |||
| latitude | 99 | 100% | 99 | |||
| longitude | 99 | 100% | 99 | |||
| sex | 99 | 100% | 99 | |||
| age_at_collection_days | 98 | 99% | 98 | |||
| bmi | 89 | 90% | 89 | |||
| detailed_location | 61 | 62% | ||||
| location_region | 61 | 62% | 61 |
- Data on gut metagenomes of the patients with alcoholic dependence syndrome and alcoholic liver cirrhosis. 2017 PMID 28138508 PMC5257029 own_data
- Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease. 2017 PMID 29041989 PMC5645934 own_data
- Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies. 2022 PMID 35168645 PMC8845349 unsure
Archive description
Stool samples were collected from the patients with alcohol dependence syndrome and alcoholic liver cirrhosis from Russian Federation, subject to total DNA extraction and whole-genome metagenomic sequencing using SOLiD 5500xl platform.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host study.description · “Stool samples were collected from the patients”
- body site study.description · “Stool samples were collected”
- life stage study.title · “patients with alcohol dependence syndrome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA4555478 | age_at_collection_days | 14244.8 | R2 | 0.80 | paper.supp.40168_2017_359_MOESM1_ESM.xlsx[Table S1][nan] | 39 |
| SAMEA4555477 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | antibiotics and proton pump inhibitors) less than 1 month prior |
| SAMEA4555477 | bmi | 21.67 | R2 | 0.80 | paper.supp.40168_2017_359_MOESM1_ESM.xlsx[Table S1][nan] | 21.67 |
| SAMEA4555477 | collection_date | 2015 | R1 | 0.90 | biosample.attribute:collection_date | 2015 |
| SAMEA4555477 | country | RU | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Russia |
| SAMEA4555477 | health_condition | neurological_psychiatric | R2 | 0.80 | paper.supp.40168_2017_359_MOESM1_ESM.xlsx[Table S1][nan] | ADS |
| SAMEA4555477 | health_condition_detail | ADS | R2 | 0.80 | paper.supp.40168_2017_359_MOESM1_ESM.xlsx[Table S1][nan] | ADS |
| SAMEA4555477 | latitude | 59.9500 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | N59�57 E30�18 |
| SAMEA4555509 | location_region | Tatarstan | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | N55�47 E49�07 |
| SAMEA4555477 | longitude | 30.3000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | N59�57 E30�18 |
| SAMEA4555477 | sex | male | R2 | 0.80 | paper.supp.40168_2017_359_MOESM1_ESM.xlsx[Table S1][nan] | M |
| SAMEA4555477 | subject_id | SAMEA4555477 | R3 | 0.70 | design.one_sample_per_subject:fulltext | We collected 99 stool samples from the patients with alcoholic dependence syndrome (n=72) and alcoholic liver cirrhosis (n=27) |
Sequencing
99 runs over 99 samples · mean 1.29 Gbp per run (median 1.06 Gbp, total 127.51 Gbp; 99 runs with a base count) · layout SINGLE 99 · platform ABI_SOLID 99 · models AB 5500xl Genetic Analyzer (99) · 0% of runs with a Sandpiper profile · first public 2016-12-06
Authors (33)
Tyakht AV first · Dubinkina VB · Odintsova VY · Yarygin KS · Kovarsky BA · Pavlenko AV · Ischenko DS · Popenko AS · Alexeev DG · Taraskina AY · Nasyrova RF · Krupitski EM · Shalikiani NV · Bakulin IG · Shcherbakov PL · Skorodumova LO · Larin AK · Kostryukova ES · Abdulkhakov RA · Abdulkhakov SR · Malanin SY · Ismagilova RK · Grigoryeva TV · Ilina EN · Govorun VM last · Krupitsky EM · Naseri M first · Palizban F · Yadegar A · Khodarahmi M · Asadzadeh Aghdaei H · Houri H · Zahiri J last
Downloads
PRJEB18041.csv.gz (4.2 KB) · parquet (76.4 KB) — all 99 samples, every field with route and confidence · PRJEB18041_determinations.csv.gz (8.6 KB) — 1,139 evidence rows