Gut microbiome, retinopathia centralis serosa, case-control
32 stool samples from patients with retinopathia centralis serosa and healthy controls were sequenced to study gut microbiome associations with the condition, using a case-control design. machine-written summary
32 samples · 32 runs · SE · Age unknown · 2022 · 8.11 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 64 sample values (health condition, health condition detail) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC8523055 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 32 sample values (country) · 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 25 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 | 32 | 100% | 32 | |||
| health_condition | 32 | 100% | 32 | |||
| subject_id | 0 | 0% | ||||
| health_condition_detail | 32 | 100% | 32 |
- The importance of age in compositional and functional profiling of the human intestinal microbiome. 2021 PMID 34662347 PMC8523055 unsure
Archive description
To find associations between the taxonomical and functional profile of the gut metagenome and the development of retinopathia centralis Serosa (RCS), stool samples from 19 RCS patients and 19 controls with no signs of RCS were sequenced.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.85. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “stool samples from 19 RCS patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA7037039 | country | SE | R2 | 0.75 | external.gmrepo source | country: Sweden |
| SAMEA7037039 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:description | description: control |
| SAMEA7037039 | health_condition_detail | control | R1 | 0.85 | biosample.attribute:description | description: control |
Sequencing
32 runs over 32 samples · mean 8.88 Gbp per run (median 8.11 Gbp, total 284.12 Gbp; 32 runs with a base count) · layout PAIRED 32 · platform ILLUMINA 32 · models Illumina HiSeq 3000 (32) · 78% of runs with a Sandpiper profile · first public 2022-06-28
Authors (6)
Herzog EL first · Wäfler M · Keller I · Wolf S · Zinkernagel MS · Zysset-Burri DC last
Downloads
PRJEB38997.csv.gz (1.6 KB) · parquet (69.5 KB) — all 32 samples, every field with route and confidence · PRJEB38997_determinations.csv.gz (1.1 KB) — 96 evidence rows