Gut metagenomes in Crohn's disease vs healthy controls
Whole-community shotgun sequencing of 11 human stool samples (7 from healthy individuals, 4 from donors with Crohn's disease), used in a case-control design to benchmark metagenomic analysis pipelines. machine-written summary
11 samples · 11 runs · Age unknown · 2012 · 0.12 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 22 sample values (health condition, health condition detail) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC4269443, PMC6759048, PMC8940201 |
| ○ 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 6 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 | 0 | 0% | ||||
| country | 0 | 0% | ||||
| health_condition | 11 | 100% | 11 | |||
| subject_id | 0 | 0% | ||||
| health_condition_detail | 11 | 100% | 11 |
- MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences. 2022 PMID 35330728 PMC8940201 own_data
- Bacterial bile metabolising gene abundance in Crohn's, ulcerative colitis and type 2 diabetes metagenomes. 2014 PMID 25517115 PMC4269443 unsure
- Microbial genes and pathways in inflammatory bowel disease. 2019 PMID 31249397 PMC6759048 unsure
Archive description
Whole community shotgun sequencing of 11 human stool samples (7 healthy and 4 from donors with Crohn's disease).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.85. Assay shotgun_dna.
- host study.description · “11 human stool samples”
- body site study.description · “11 human stool samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN01178398 | health_condition | crohns_disease | R1 | 0.90 | biosample_attr | Crohn's Disease |
| SAMN01178402 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:title | Healthy Sample 7844 for Homo sapiens |
| SAMN01178398 | health_condition_detail | Crohn's Disease | R1 | 0.90 | sample.attr.health_state | Crohn's Disease |
| SAMN01178402 | health_condition_detail | Healthy | R1 | 0.70 | sample.name_rule:title | Healthy Sample 7844 for Homo sapiens |
Sequencing
11 runs over 11 samples · mean 0.12 Gbp per run (median 0.12 Gbp, total 1.31 Gbp; 11 runs with a base count) · layout PAIRED 11 · platform ILLUMINA 11 · models Illumina MiSeq (11) · 55% of runs with a Sandpiper profile · first public 2012-10-29
Authors (14)
Labbé A first · Ganopolsky JG · Martoni CJ · Prakash S · Jones ML last · Schirmer M first · Garner A · Vlamakis H · Xavier RJ last · Morais DAA first · Cavalcante JVF · Monteiro SS · Pasquali MAB · Dalmolin RJS last
Downloads
PRJNA175224.csv.gz (1.1 KB) · parquet (68.8 KB) — all 11 samples, every field with route and confidence · PRJNA175224_determinations.csv.gz (648 B) — 22 evidence rows