Host DNA depletion methods in gut biopsies, Switzerland
One endoscopic biopsy sample from a healthy adult in Switzerland was used to compare host DNA depletion kits and Oxford Nanopore adaptive sampling for microbiome shotgun sequencing. machine-written summary
78 samples · 78 runs · CH · Adult · 2023 · 5.86 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 312 sample values (antibiotic exposure, country, health condition, health condition detail) · PMC10169731 |
| ○ 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 | 78 | 100% | ||||
| country | 78 | 100% | 78 | |||
| health_condition | 78 | 100% | 78 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 78 | 100% | 78 | |||
| health_condition_detail | 78 | 100% | 78 |
- Benchmarking microbial DNA enrichment protocols from human intestinal biopsies. 2023 PMID 37180976 PMC10169731 own_data
Archive description
We have used several kits and Oxford Nanopore sequencing with adaptive sampling to see which method is the best to deplete host DNA from endoscopical biopsies from human
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids 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 · “depletion from human intestinal samples”
- body site study.description · “DNA from endoscopical biopsies from human”
- 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 |
|---|---|---|---|---|---|---|
| SRR23814916 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | none of the participants had taken antibiotics |
| SRR23814916 | country | CH | R3 | 0.70 | paper.fulltext.methods | Bern Cantonal Ethics Commission |
| SRR23814916 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | without any gastrointestinal symptoms and without functional intestinal symptoms |
| SRR23814916 | health_condition_detail | without any gastrointestinal symptoms...negative results in all additional workups | R3 | 0.70 | paper.fulltext.methods | without any gastrointestinal symptoms and without functional intestinal symptoms |
Sequencing
78 runs over 78 samples · mean 6.74 Gbp per run (median 5.86 Gbp, total 526.06 Gbp; 78 runs with a base count) · layout PAIRED 68, SINGLE 10 · platform ILLUMINA 68, OXFORD_NANOPORE 10 · models Illumina NovaSeq 6000 (68), GridION (10) · 68% of runs with a Sandpiper profile · first public 2023-03-13 – 2023-03-17
Authors (5)
Marchukov D first · Li J · Juillerat P · Misselwitz B · Yilmaz B last
Downloads
PRJNA943380.csv.gz (2.6 KB) · parquet (72.0 KB) — all 78 samples, every field with route and confidence · PRJNA943380_determinations.csv.gz (1.7 KB) — 312 evidence rows