Matrix-tube vs plate extraction method validation, San Diego
384 samples from San Diego, CA (336 adults, 48 infants) comparing a Matrix-tube-based nucleic acid extraction pipeline against a benchmarked plate-based method; no health condition or intervention specified. machine-written summary
336 samples · 576 runs · US · Adult · 2023 · 1.12 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,895 sample values (country, location locality, location region, sex, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11494942, PMC12584695 |
| ○ 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 |
longitudinal — not resolved
5 of 46 people sampled more than once (80 samples; median 12, up to 32 per person).
Genera, mean relative abundance over 89 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 | 336 | 100% | ||||
| country | 336 | 100% | 336 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 336 | 100% | 336 | |||
| detailed_location | 336 | 100% | ||||
| location_locality | 336 | 100% | 336 | |||
| location_region | 336 | 100% | 336 | |||
| timepoint_label | 336 | 100% | 336 | |||
| sex | 215 | 64% | 215 |
- Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies. 2024 PMID 39283083 PMC11494942 own_data
- Streamlined extraction of nucleic acids and metabolites from low- and high-biomass samples using isopropanol and matrix tubes. 2025 PMID 41070991 PMC12584695 own_data
Archive description
Goal: to reduce the hands-on time for the nucleic acid extraction pipeline, enabling processing of 10000 samples per month. Reduce the cost per extraction and reduce the well to well contamination.
How this project entered the registry
Classified as human and non-human (mixed) gut / stool / oral cavity / skin / multiple sites shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.scientific_name · “human oral metagenome”
- host run.scientific_name · “mouse gut metagenome”
- body site run.scientific_name · “human oral metagenome”
- body site run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human skin metagenome”
- life stage sample.attr.host_life_stage · “adult (n=263/384)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA111486423 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:CA: San Diego |
| SAMEA111486423 | location_locality | San Diego | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:CA: San Diego |
| SAMEA111486423 | location_region | California | R1 | 0.75 | biosample.attribute:geo_loc_name | USA:CA: San Diego |
| SAMEA111486423 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMEA111486423 | subject_id | C | R1 | 0.85 | sample.attr.host_subject_id | C |
| SAMEA111486423 | timepoint_label | 1_2 | R1 | 0.85 | sample.attr.round | 1_2 |
Sequencing
576 runs over 336 samples · mean 1.35 Gbp per run (median 1.14 Gbp, total 776.58 Gbp; 576 runs with a base count) · layout PAIRED 576 · platform ILLUMINA 576 · models Illumina NovaSeq 6000 (576) · 39% of runs with a Sandpiper profile · first public 2023-01-05 – 2025-06-12
Authors (28)
Brennan C first · Belda-Ferre P · Zuffa S · Charron-Lamoureux V · Mohanty I · Ackermann G · Allaband C · Ambre M · Boyer T · Bryant M · Cantrell K · Gonzalez A · McDonald D · Salido RA · Song SJ · Wright G · Dorrestein PC · Knight R last · Shaffer JP · Weng Y · Farmer S · González A · Martino C · Meehan MJ · Rahman G · Schwartz T · Tribelhorn C · Tubb HM
Downloads
PRJEB56784.csv.gz (8.2 KB) · parquet (80.5 KB) — all 336 samples, every field with route and confidence · PRJEB56784_determinations.csv.gz (9.5 KB) — 1,895 evidence rows