Gut metagenomes in Sjögren syndrome and dry eye, USA
34 stool samples from adults in the USA, comparing healthy controls (20), Sjögren syndrome/autoimmune inflammatory cases (7), and other dry eye cases (7) in a case-control design. machine-written summary
34 samples · 34 runs · US · Adult · 2023 · 0.28 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 238 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 68 sample values (location site, sex) · PMC8959809 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 | 34 | 100% | ||||
| country | 34 | 100% | 34 | |||
| health_condition | 34 | 100% | 34 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 34 | 100% | 34 | |||
| detailed_location | 34 | 100% | ||||
| health_condition_detail | 34 | 100% | 34 | |||
| latitude | 34 | 100% | 34 | |||
| location_region | 34 | 100% | 34 | |||
| location_site | 34 | 100% | 34 | |||
| longitude | 34 | 100% | 34 | |||
| sex | 34 | 100% | 34 |
- Gut Microbiota From Sjögren syndrome Patients Causes Decreased T Regulatory Cells in the Lymphoid Organs and Desiccation-Induced Corneal Barrier Disruption in Mice. 2022 PMID 35355610 PMC8959809 own_data
Archive description
Metagenomic sequencing from human patient stool samples to identify bacterial taxa that are enriched or depleted in patients with Sjogren syndrome and dry eye
How this project entered the registry
Classified as human gut / stool / eye / ear shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Human gut metagenomic sequencing from”
- body site study.description · “from human patient stool samples to identify”
- body site study.title · “Sjogren Syndrome, dry eye and healthy control”
- body site study.description · “syndrome and dry eye”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN25275985 | collection_date | 2019-02-15 | R1 | 0.90 | biosample.attribute:collection_date | 2019-02-15 |
| SAMN25275985 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN25275985 | health_condition | autoimmune_inflammatory | R1 | 0.70 | sample.name_rule:title | 1901 Sjogren Syndrome human stool sample |
| SAMN25275985 | health_condition_detail | Sjogren Syndrome | R1 | 0.70 | sample.name_rule:title | 1901 Sjogren Syndrome human stool sample |
| SAMN25275985 | latitude | 29.7014 | R1 | 0.90 | biosample.attribute:lat_lon | 29.70139581 N 95.39352720 W |
| SAMN25275985 | location_region | Texas | R1 | 0.60 | biosample.attribute:lat_lon | 29.70139581 N 95.39352720 W |
| SAMN25275985 | location_site | Baylor College of Medicine Alkek Eye Center | R3 | 0.70 | paper.fulltext.methods | recruited from the multispecialty SS clinic at the Baylor College of Medicine |
| SAMN25275985 | longitude | -95.3935 | R1 | 0.90 | biosample.attribute:lat_lon | 29.70139581 N 95.39352720 W |
| SAMN25275985 | sex | female | R3 | 0.70 | paper.fulltext.methods | All subjects selected for the study were female |
Sequencing
34 runs over 34 samples · mean 0.35 Gbp per run (median 0.28 Gbp, total 11.96 Gbp; 34 runs with a base count) · layout SINGLE 34 · platform ILLUMINA 34 · models Illumina NovaSeq 6000 (34) · 0% of runs with a Sandpiper profile · first public 2023-02-11
Authors (6)
Schaefer L first · Trujillo-Vargas CM · Midani FS · Pflugfelder SC · Britton RA · de Paiva CS last
Downloads
PRJNA800662.csv.gz (2.0 KB) · parquet (71.9 KB) — all 34 samples, every field with route and confidence · PRJNA800662_determinations.csv.gz (3.0 KB) — 306 evidence rows