Gut metagenome in type 1 diabetes patients in Italy
104 gut metagenome samples from subjects with type 1 diabetes, collected in Italy. machine-written summary
104 samples · 104 runs · IT · Age unknown · 2022 · 10.04 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 314 sample values (collection date, country, subject id, timepoint) |
| – Abstract / description | no abstract or project description |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| ✓ External resources | 208 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 95 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 | 104 | 100% | 104 | |||
| health_condition | 104 | 100% | 104 | |||
| subject_id | 104 | 100% | 104 | |||
| collection_date | 104 | 100% | 104 | |||
| health_condition_detail | 104 | 100% | 104 | |||
| timepoint_label | 2 | 2% | 2 |
Archive description
gut metagenome in subjects with T1-D
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”
- body site study.title · “gut metagenome and type-1 diabetes”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN29938224 | collection_date | 2022 | R1 | 0.90 | biosample.attribute:collection_date | 2022 |
| SAMN29938224 | country | IT | R1 | 0.90 | sample.attr.geo_loc_name | Italy |
| SAMN29938224 | health_condition | type1_diabetes | R2 | 0.75 | external.gmrepo source | phenotype: Diabetes Mellitus, Type 1 |
| SAMN29938224 | health_condition_detail | Diabetes Mellitus, Type 1 | R2 | 0.75 | external.gmrepo source | phenotype: Diabetes Mellitus, Type 1 |
| SAMN29938224 | subject_id | F48 | R1 | 0.70 | sample.name_rule:library_names | F48 |
| SAMN29938300 | timepoint_label | B | R1 | 0.70 | sample.name_rule:library_names | F95_B |
Sequencing
104 runs over 104 samples · mean 10.37 Gbp per run (median 10.04 Gbp, total 1,078.24 Gbp; 104 runs with a base count) · layout PAIRED 104 · platform ILLUMINA 104 · models Illumina NovaSeq 6000 (104) · 91% of runs with a Sandpiper profile · first public 2022-10-27
Authors (0)
No author record.
Downloads
PRJNA862077.csv.gz (3.5 KB) · parquet (73.8 KB) — all 104 samples, every field with route and confidence · PRJNA862077_determinations.csv.gz (4.5 KB) — 522 evidence rows