Gut virome in early-onset preeclampsia, China, case-control
31 fecal metagenome samples from pregnant women in China, including healthy controls and pregnancy/postpartum cases, studied as part of a case-control design examining the gut virome in early-onset preeclampsia. machine-written summary
31 samples · 31 runs · CN · Adult · 2022 · 9.08 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 124 sample values (collection date, country, health condition, health condition detail) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 62 sample values (sex, subject id) · PMC11036803 |
| ○ 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 28 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 | 31 | 100% | ||||
| country | 31 | 100% | 31 | |||
| health_condition | 31 | 100% | 31 | |||
| subject_id | 31 | 100% | 31 | |||
| collection_date | 31 | 100% | 31 | |||
| health_condition_detail | 31 | 100% | 31 | |||
| sex | 31 | 100% | 31 |
- Deep metagenomic characterization of the gut virome in pregnant women with preeclampsia. 2024 PMID 38506520 PMC11036803 own_data
Archive description
Preeclampsia is a pregnancy complication characterized by severe hypertension and multiple organ damage. Gut microbiota has been reported to be involved in preeclampsia by the imprecise 16S rRNA amplicon technology. To resolve the preeclampsia gut microbiota deeper and more accurately, we performed shotgun metagenomic sequencing on the fecal samples from 40 early-onset preeclampsia and 37 healthy pregnant women.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.description · “shotgun metagenomic sequencing on the fecal samples”
- life stage study.description · “early-onset preeclampsia and 37 healthy pregnant women”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA14270239 | collection_date | 2020 | R1 | 0.90 | biosample.attribute:collection_date | 2020 |
| SAMEA14270239 | country | CN | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | China |
| SAMEA14270239 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:description | gut metagenome of healthy controls |
| SAMEA14270239 | health_condition_detail | gut metagenome of healthy controls | R1 | 0.85 | biosample.attribute:description | gut metagenome of healthy controls |
| SAMEA14270239 | sex | female | R3 | 0.70 | paper.fulltext.methods | pregnant women with PE and 37 healthy pregnant women |
| SAMEA14270239 | subject_id | SAMEA14270239 | R3 | 0.75 | design.one_sample_per_subject:fulltext | a single cross-sectional study cannot provide causality evidence |
Sequencing
31 runs over 31 samples · mean 9.54 Gbp per run (median 9.08 Gbp, total 295.82 Gbp; 31 runs with a base count) · layout PAIRED 31 · platform ILLUMINA 31 · models Illumina HiSeq X (31) · 90% of runs with a Sandpiper profile · first public 2022-04-28 – 2022-05-06
Authors (15)
Lv LJ first · Wen JY · Zhang Y · Guo RC · Li H · Yi ZT · He TW · Chen MC · Chen Y · Wu XY · Li Sh · Kang J · Hou YP · Yan Ql · Yin AH last
Downloads
PRJEB52189.csv.gz (1.8 KB) · parquet (70.7 KB) — all 31 samples, every field with route and confidence · PRJEB52189_determinations.csv.gz (1.9 KB) — 186 evidence rows