Gut metagenomes in Crohn's disease case-control study, China
Metagenomic analysis of 31 gut samples from China, studying Crohn's disease; archive description reports a gene (DL-endopeptidase) with reduced abundance in CD, negatively correlated with colitis activity. Design: case-control. machine-written summary
31 samples · 31 runs · CN · Adult · 2024 · 14.38 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 155 sample values (collection date, country, health condition, health condition detail, subject id) |
| ○ 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 |
longitudinal — not resolved
2 of 29 people sampled more than once (4 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 26 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 |
- Gut microbial DL-endopeptidase alleviates Crohn's disease via the NOD2 pathway. 2022 PMID 36049483 own_data
Archive description
Metagenomic analysis of CD cohorts from China (n=29) revealed that DL-endopeptidase gene abundance decreased in CD and negatively correlated with colitis activities.
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.title · “Gut microbial DL-endopeptidase protects”
- 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 |
|---|---|---|---|---|---|---|
| SAMEA115395211 | collection_date | 2021 | R1 | 0.90 | biosample.attribute:collection_date | 2021 |
| SAMEA115395211 | country | CN | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | China |
| SAMEA115395211 | health_condition | crohns_disease | R1 | 0.70 | sample.name_rule:title | Sample-CD1 |
| SAMEA115395211 | health_condition_detail | Crohn's disease patient (CD cohort per study title/description) | R1 | 0.70 | sample.name_rule:title | Sample-CD1 |
| SAMEA115395211 | subject_id | CD1 | R1 | 0.70 | sample.name_rule:title | Sample-CD1 |
Sequencing
31 runs over 31 samples · mean 13.91 Gbp per run (median 14.38 Gbp, total 431.27 Gbp; 31 runs with a base count) · layout PAIRED 31 · platform ILLUMINA 31 · models Illumina MiSeq (31) · 84% of runs with a Sandpiper profile · first public 2024-03-14
Authors (0)
No author record.
Downloads
PRJEB51945.csv.gz (1.8 KB) · parquet (70.4 KB) — all 31 samples, every field with route and confidence · PRJEB51945_determinations.csv.gz (1.8 KB) — 155 evidence rows