Gut metagenomics in lean vs non-lean NAFLD, Shanghai
61 gut metagenome samples from Zhangjiang, Sanlin and Beicai communities in Shanghai, China, comparing lean and non-lean NAFLD groups using a case-control design with clinical biochemical correlation. machine-written summary
61 samples · 61 runs · CN · Age unknown · 2023 · 11.36 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 363 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ✓ Abstract / description | 122 sample values (location site, subject id) |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| ✓ External resources | 122 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 |
Genera, mean relative abundance over 55 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 | 61 | 100% | 61 | |||
| health_condition | 61 | 100% | 61 | |||
| subject_id | 61 | 100% | 61 | |||
| collection_date | 61 | 100% | 61 | |||
| detailed_location | 61 | 100% | ||||
| health_condition_detail | 61 | 100% | 61 | |||
| latitude | 61 | 100% | 61 | |||
| location_locality | 61 | 100% | 61 | |||
| location_site | 61 | 100% | 61 | |||
| longitude | 61 | 100% | 61 | |||
| location_region | 58 | 95% | 58 |
Archive description
In this research, a total of 61 samples were selected from Zhangjiang, Sanlin and Beicai communities respectively, and divided into lean NAFLD and non-lean NAFLD groups using a case-control study, and correlation analysis was performed by intestinal macrogenomics and clinical biochemical indicators to identify key characteristics of lean NAFLD population.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “intestinal macrogenomics”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN33603809 | collection_date | 2018-07-20 | R1 | 0.90 | biosample.attribute:collection_date | 2018-07-20 |
| SAMN33603809 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China: Shanghai |
| SAMN33603809 | health_condition | cardiometabolic_other | R2 | 0.75 | external.gmrepo source | phenotype: Non-alcoholic Fatty Liver Disease |
| SAMN33603809 | health_condition_detail | Non-alcoholic Fatty Liver Disease | R2 | 0.75 | external.gmrepo source | phenotype: Non-alcoholic Fatty Liver Disease |
| SAMN33603809 | latitude | 31.7444 | R1 | 0.90 | biosample.attribute:lat_lon | 31.7444 N 121.1712 E |
| SAMN33603809 | location_locality | Shanghai | R1 | 0.85 | biosample.attribute:geo_loc_name | China: Shanghai |
| SAMN33603812 | location_region | Shanghai Shi | R1 | 0.60 | biosample.attribute:lat_lon | 31.7444 N 121.1713 E |
| SAMN33603809 | location_site | Zhangjiang, Sanlin, Beicai communities | R4 | 0.45 | ena.study_description | Zhangjiang, Sanlin and Beicai communities |
| SAMN33603809 | longitude | 121.1712 | R1 | 0.90 | biosample.attribute:lat_lon | 31.7444 N 121.1712 E |
| SAMN33603809 | subject_id | SAMN33603809 | R4 | 0.65 | design.one_sample_per_subject:description | selected from Zhangjiang, Sanlin and Beicai communities respectively, and divided into lean NAFLD and non-lean NAFLD groups using a case-control study |
Sequencing
61 runs over 61 samples · mean 11.47 Gbp per run (median 11.36 Gbp, total 699.89 Gbp; 61 runs with a base count) · layout PAIRED 61 · platform ILLUMINA 61 · models Illumina NovaSeq 6000 (61) · 90% of runs with a Sandpiper profile · first public 2023-03-17
Authors (0)
No author record.
Downloads
PRJNA941376.csv.gz (2.8 KB) · parquet (73.7 KB) — all 61 samples, every field with route and confidence · PRJNA941376_determinations.csv.gz (5.9 KB) — 607 evidence rows