Fecal DNA extraction protocol comparison, Copenhagen
233 DNA samples from a mock microbial community and fecal samples of 6 individuals in Copenhagen, Denmark, comparing five DNA extraction protocols against a standardized method; cross-sectional design. machine-written summary
233 samples · 234 runs · DK · Age unknown · 2020 · 12.17 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,398 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10084625, PMC7355182 |
| ✓ Supplementary tables | 617 sample values (age, sex, subject id) |
| – 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
7 of 7 people sampled more than once (223 samples; median 30, up to 36 per person).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 197 | 85% | ||||
| country | 233 | 100% | 233 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 223 | 96% | 223 | |||
| collection_date | 233 | 100% | 233 | |||
| detailed_location | 233 | 100% | ||||
| latitude | 233 | 100% | 233 | |||
| location_locality | 233 | 100% | 233 | |||
| location_region | 233 | 100% | 233 | |||
| longitude | 233 | 100% | 233 | |||
| age_at_collection_days | 197 | 85% | 197 | |||
| sex | 197 | 85% | 197 |
- Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes. 2023 PMID 37032329 PMC10084625 own_data
- Assessment of fecal DNA extraction protocols for metagenomic studies. 2020 PMID 32657325 PMC7355182 unsure
Archive description
Aiming at providing an alternative method for human fecal DNA extraction, this study compared 5 DNA extraction protocols (MagPure Stool DNA KF Kit (MP), Macherey-Nagel Nucleospin Soil kit (MN), Zymo Research Quick-DNATM Fecal/Soil Microbe kit (ZYMO), MOBIO DNeasy PowerSoil protocol (PS) and MetaHIT) with a standardized protocol Q using 1 microbial mock community (MMC) (contained 8 bacterial and 2 fungal strains) and fecal samples from 6 individuals via shotgun metagenomics sequencing. For each protocol, six technical replicates were generated on the MMC and each human fecal sample. In total, 233 qualified DNA samples (36 MMC extractions and 197 human fecal DNA extractions) were subjected to shotgun sequencing and further quantitative analyses.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host study.description · “human fecal DNA extraction”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA6804738 | age_at_collection_days | 12784.0 | R2 | 0.80 | paper.supp.Supplementary Tables S1-9.xlsx[ST2!Age(years)] | SampleID=E-39; Age(years)=35 |
| SAMEA6804736 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMEA6804736 | country | DK | R1 | 0.90 | sample.attr.geographic_location | Denmark: Copenhagen |
| SAMEA6804736 | latitude | 55.6800 | R1 | 0.90 | biosample.attribute:latitude_and_longitude | 55.68 N 12.57 E |
| SAMEA6804736 | location_locality | Copenhagen | R1 | 0.85 | biosample.attribute:geographic_location | Denmark: Copenhagen |
| SAMEA6804736 | location_region | Capital Region | R1 | 0.60 | biosample.attribute:latitude_and_longitude | 55.68 N 12.57 E |
| SAMEA6804736 | longitude | 12.5700 | R1 | 0.90 | biosample.attribute:latitude_and_longitude | 55.68 N 12.57 E |
| SAMEA6804738 | sex | female | R2 | 0.80 | paper.supp.Supplementary Tables S1-9.xlsx[ST2!Gender] | SampleID=E-39; Gender=Female |
| SAMEA6804737 | subject_id | D6300 | R2 | 0.80 | paper.supp.Supplementary Tables S1-9.xlsx[ST2!Sample] | SampleID=D6300-30; Sample=D6300 |
Sequencing
234 runs over 233 samples · mean 12.42 Gbp per run (median 12.18 Gbp, total 2,905.32 Gbp; 234 runs with a base count) · layout PAIRED 234 · platform BGISEQ 234 · models BGISEQ-500 (234) · 0% of runs with a Sandpiper profile · first public 2020-05-25
Authors (18)
Yang F first · Sun J · Luo H · Ren H · Zhou H · Lin Y · Han M · Chen B · Liao H · Brix S · Li J · Yang H · Kristiansen K · Zhong H last · Bazant W first · Blevins AS · Crouch K · Beiting DP last
Downloads
PRJEB38036.csv.gz (6.2 KB) · parquet (77.6 KB) — all 233 samples, every field with route and confidence · PRJEB38036_determinations.csv.gz (13.7 KB) — 2,015 evidence rows