Gut virome in SLE patients vs controls, China (case-control)
44 fecal samples from adults in China, comparing gut virome composition between systemic lupus erythematosus patients and healthy controls using bulk and VLP metagenomic sequencing in a case-control design. machine-written summary
44 samples · 44 runs · CN · Adult · 2022 · 4.11 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 308 sample values (collection date, country, health condition, health condition detail, latitude, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC9874095 |
| ○ 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 |
Genera, mean relative abundance over 38 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 | 44 | 100% | ||||
| country | 44 | 100% | 44 | |||
| health_condition | 44 | 100% | 44 | |||
| subject_id | 44 | 100% | 44 | |||
| collection_date | 44 | 100% | 44 | |||
| health_condition_detail | 44 | 100% | 44 | |||
| latitude | 44 | 100% | 44 | |||
| longitude | 44 | 100% | 44 |
- Alterations of the gut virome in patients with systemic lupus erythematosus. 2022 PMID 36713446 PMC9874095 own_data
Archive description
Systemic lupus erythematosus (SLE) is a systemic autoimmune disease that has been linked to the dysbiosis of the gut microbiome and virome. However, the potential characterization of the gut virome in SLE patients needs to be unexplored more extensively. Herein, we analyzed the gut viral community of 16 SLE patients and 31 healthy controls using both bulk and virus-like particle (VLP)-based metagenomic sequencing of their fecal samples. A total of 15,999 non-redundant viral operational taxonomic units (vOTUs) were identified from the metagenomic assembled contigs and used for gut virome profiling.
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 · “dysbiosis of the gut microbiome and virome.”
- 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 |
|---|---|---|---|---|---|---|
| SAMEA111520296 | collection_date | 2021 | R1 | 0.90 | biosample.attribute:collection_date | 2021 |
| SAMEA111520296 | country | CN | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | China |
| SAMEA111520296 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:DESCRIPTION | gut virome of healthy controls |
| SAMEA111520296 | health_condition_detail | gut virome of healthy controls | R1 | 0.85 | biosample.attribute:DESCRIPTION | gut virome of healthy controls |
| SAMEA111520296 | latitude | 26.0000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 26 106 |
| SAMEA111520296 | longitude | 106.0000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 26 106 |
| SAMEA111520296 | subject_id | HC01 | R1 | 0.70 | sample.name_rule:alias | gz_HC01-V |
Sequencing
44 runs over 44 samples · mean 4.67 Gbp per run (median 4.11 Gbp, total 205.68 Gbp; 44 runs with a base count) · layout PAIRED 44 · platform ILLUMINA 44 · models Illumina NovaSeq 6000 (44) · 86% of runs with a Sandpiper profile · first public 2022-10-27
Authors (21)
Chen C first · Yan Q · Yao X · Li S · Lv Q · Wang G · Zhong Q · Tang F · Liu Z · Huang Y · An Y · Zhou J · Zhang Q · Zhang A · Ullah H · Zhang Y · Liu C · Zhu D · Li H · Sun W · Ma W last
Downloads
PRJEB55711.csv.gz (2.0 KB) · parquet (71.2 KB) — all 44 samples, every field with route and confidence · PRJEB55711_determinations.csv.gz (2.7 KB) — 308 evidence rows