Gut metagenomics in new-onset rheumatoid arthritis, Nanjing
Case-control shotgun metagenomics of 47 gut microbiome samples from Nanjing, China, comparing treatment-naive new-onset rheumatoid arthritis patients (25) with healthy controls (22). machine-written summary
47 samples · 47 runs · CN · Adult · 2022 · 6.03 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 235 sample values (collection date, country, health condition, health condition detail, location locality) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 45 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 | 47 | 100% | ||||
| country | 47 | 100% | 47 | |||
| health_condition | 47 | 100% | 47 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 47 | 100% | 47 | |||
| detailed_location | 47 | 100% | ||||
| health_condition_detail | 47 | 100% | 47 | |||
| location_locality | 47 | 100% | 47 |
- Gut commensal Parabacteroides distasonis alleviates inflammatory arthritis. 2023 PMID 36604114 own_data
Archive description
From shotgun metagenomics of treatment-naive rheumatoid arthritis (RA) patients with new-onset RA, we found 8308 species of gut microbiota, and 999 differential species of gut microbiota. Among them, 861 species are significantly upregulated and 138 species are significantly downregulated compared with that in healthy subjects.
How this project entered the registry
Classified as human gut / stool 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.description · “8308 species of gut microbiota, and 999”
- body site external_curation.infant_catalog · “body_site_call gut”
- 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 |
|---|---|---|---|---|---|---|
| SAMN31542354 | collection_date | 2020-01-01 | R1 | 0.90 | biosample.attribute:collection_date | 2020-01-01 |
| SAMN31542354 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China:NanJing |
| SAMN31542354 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:sample_alias | Normal_01 |
| SAMN31542354 | health_condition_detail | Normal | R1 | 0.70 | sample.name_rule:sample_alias | Normal_01 |
| SAMN31542354 | location_locality | Nanjing | R1 | 0.85 | biosample.attribute:geo_loc_name | China:NanJing |
Sequencing
47 runs over 47 samples · mean 6.08 Gbp per run (median 6.03 Gbp, total 285.63 Gbp; 47 runs with a base count) · layout PAIRED 47 · platform ILLUMINA 47 · models Illumina NovaSeq 6000 (47) · 96% of runs with a Sandpiper profile · first public 2022-12-27
Authors (0)
No author record.
Downloads
PRJNA896336.csv.gz (2.0 KB) · parquet (70.6 KB) — all 47 samples, every field with route and confidence · PRJNA896336_determinations.csv.gz (2.4 KB) — 235 evidence rows