Gut phageome in type 2 diabetes, Shanghai, China
A gut metagenome sample from Shanghai, China, studied for enteric phageome alterations associated with type 2 diabetes; design listed as "other." machine-written summary
46 samples · 46 runs · CN · Age unknown · 2019 · 11.23 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 92 sample values (health condition, health condition detail) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 138 sample values (antibiotic exposure, country, location region) · PMC7862107 |
| ✓ Supplementary tables | 34 sample values (bmi, medication) |
| – 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 1 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 | 46 | 100% | 46 | |||
| health_condition | 46 | 100% | 46 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 46 | 100% | 46 | |||
| detailed_location | 46 | 100% | ||||
| health_condition_detail | 46 | 100% | 46 | |||
| location_region | 46 | 100% | 46 | |||
| bmi | 17 | 37% | 17 | |||
| medication | 17 | 37% | 17 |
- Enteric Phageome Alterations in Patients With Type 2 Diabetes. 2020 PMID 33552999 PMC7862107 own_data
Archive description
Enteric phageome alternations in Type 2 diabetes disease
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “human gut metagenome Metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SRR10479802 | antibiotic_exposure | no | R3 | 0.70 | paper.body.methods | Those who received antibiotics in the preceding 3 months were excluded from this study. |
| SRR10479802 | bmi | 27.58 | R2 | 0.80 | paper.supp.DataSheet_1.docx[Supplementary Table 6!height (cm);Weight (kg)] | subject D10: height 166 cm, weight 76 kg |
| SRR10479802 | country | CN | R3 | 0.70 | paper.body.methods | Patients with T2D involved in this study were recruited from Shanghai Jiao Tong University Affiliated Sixth People’s Hospital. |
| SRR10479802 | health_condition | type2_diabetes | R1 | 0.70 | sample.name_rule:library_name | library_name: D10 |
| SRR10479802 | health_condition_detail | T2D | R1 | 0.70 | sample.name_rule:library_name | library_name: D10 |
| SRR10479802 | location_region | Shanghai | R3 | 0.70 | paper.body.methods | Healthy volunteers aged 20 to 50 years old in the control group were recruited from Shanghai Jiao Tong University Affiliated Sixth People’s Hospital. |
| SRR10479802 | medication | antidiabetic_other;metformin;statin | R2 | 0.85 | paper.supp.DataSheet_1.docx[Supplementary Tables 7-8!drug columns =1] | subject D10: Insulin, Metformin, Statin, TZD = 1 |
Sequencing
46 runs over 46 samples · mean 11.72 Gbp per run (median 11.23 Gbp, total 539.07 Gbp; 46 runs with a base count) · layout PAIRED 46 · platform ILLUMINA 46 · models HiSeq X Ten (46) · 91% of runs with a Sandpiper profile · first public 2019-11-19
Authors (0)
No author record.
Downloads
PRJNA588627.csv.gz (2.0 KB) · parquet (70.9 KB) — all 46 samples, every field with route and confidence · PRJNA588627_determinations.csv.gz (3.7 KB) — 264 evidence rows