Meta3C linking of ARGs to gut bacterial hosts (IBD, n=1)
Meta3C chromosome-conformation-capture shotgun metagenomic sequencing, with spike-in controls, of a single human stool sample from an individual with inflammatory bowel disease, used to link antimicrobial resistance genes to their bacterial hosts. machine-written summary
1 samples · 2 runs · Age unknown · 2022 · 28.28 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3 sample values (collection date, health condition, health condition detail) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 1 sample values (subject id) · PMC10327510 |
| ○ 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 |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 0 | 0% | ||||
| health_condition | 1 | 100% | 1 | |||
| subject_id | 1 | 100% | 1 | |||
| collection_date | 1 | 100% | 1 | |||
| health_condition_detail | 1 | 100% | 1 |
- Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts 2023 PMID 37272920 PMC10327510 own_data
Archive description
This project aimed to use meta3C and Hi-C data to reliably link antimicrobial resistance genes to their microbial hosts. To this aim, we generated a meta3C dataset, using spike-in controls, of a human stool sample.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by curator_audit with confidence 0.60. Assay shotgun_dna.
- host description · “meta3C dataset, using spike-in controls, of a human stool sample”
- host runs.scientific_name · “human gut metagenome (2)”
- body site description · “meta3C dataset, using spike-in controls, of a human stool sample”
- body site runs.scientific_name · “human gut metagenome (2)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN30791700 | collection_date | 2016 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2016 |
| SAMN30791700 | health_condition | ibd_unspecified | R1 | 0.85 | biosample.attribute:gastrointest_disord | gastrointest_disord: IBD |
| SAMN30791700 | health_condition_detail | IBD | R1 | 0.85 | biosample.attribute:gastrointest_disord | gastrointest_disord: IBD |
| SAMN30791700 | subject_id | SAMN30791700 | R3 | 0.70 | design.one_sample_per_subject:fulltext | The stool sample used to create a meta3C library was obtained from a patient with inflammatory bowel disease |
Sequencing
2 runs over 1 samples · mean 14.14 Gbp per run (median 14.14 Gbp, total 28.28 Gbp; 2 runs with a base count) · layout PAIRED 2 · platform ILLUMINA 2 · models NextSeq 550 (2) · 50% of runs with a Sandpiper profile · first public 2022-09-12
Authors (0)
No author record.
Downloads
PRJNA879122.csv.gz (872 B) · parquet (68.9 KB) — all 1 samples, every field with route and confidence · PRJNA879122_determinations.csv.gz (575 B) — 4 evidence rows