Nucleic acid extraction protocol comparison, San Diego, CA
2,770 samples from diverse environmental and host-associated sources (including body sites) in San Diego, CA, USA, compared across two total nucleic acid extraction protocols versus a prior benchmark protocol in an intervention design. machine-written summary
1,971 samples · 2,770 runs · US · Age unknown · 2020 · 47.2 Mbp / sample · cohort Contamination source modeling with SCRuB improves
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 12,592 sample values (age, bmi, country, location locality, location region, sex, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10504420, PMC7931620, PMC9361692 |
| ○ 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
33 of 175 people sampled more than once (738 samples; median 18, up to 60 per person) · follow-up median 2.0 y (max 2.0 y) · median interval between samples 2.0 y (time from age at collection).
Each row is one person (2 shown of 33); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 64 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 | 1,223 | 62% | ||||
| country | 1,971 | 100% | 1,971 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 1,971 | 100% | 1,971 | |||
| detailed_location | 1,971 | 100% | ||||
| location_locality | 1,971 | 100% | 1,971 | |||
| location_region | 1,971 | 100% | 1,971 | |||
| timepoint_label | 1,971 | 100% | 1,971 | |||
| sex | 1,139 | 58% | 1,139 | |||
| age_at_collection_days | 954 | 48% | 954 | |||
| bmi | 644 | 33% | 644 |
- A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities. 2021 PMID 33512248 PMC7931620 own_data
- A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities. 2022 PMID 35713407 PMC9361692 own_data
- A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities 2020 own_data
- A comparison of six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing of microbial communities 2022 own_data
- Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data. 2023 PMID 36928429 PMC10504420 unsure
Archive description
Our DNA extraction protocol is years old, and we want to compare new extraction methods to address outstanding issues. For more details, check out the motivation and experimental design here: https://docs.google.com/document/d/1qbuySJLEpxQjql-P6kJOk8QOS7Uo3MS1CL3QT56sDXI/edit?usp=sharing
How this project entered the registry
Classified as human and non-human (mixed) gut / stool / skin / oral cavity shotgun DNA metagenome of adult by opus_adjudicated with confidence 0.50. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.host_tax_id · “10090”
- host run.scientific_name · “synthetic metagenome”
- body site sample.attr.host_body_habitat · “stool (n=439/2770)”
- body site sample.attr.host_body_habitat · “UBERON:skin (n=398/2770)”
- body site sample.attr.host_body_habitat · “oral (n=342/2770)”
- life stage sample.attr.host_life_stage · “adult (n=1486/2770)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA12935406 | age_at_collection_days | 11322.8 | R1 | 0.90 | sample.attr.host_age | 31 |
| SAMEA12935406 | bmi | 20.5 | R1 | 0.90 | sample.attr.host_body_mass_index | 20.5 |
| SAMEA12935190 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:CA:San Diego |
| SAMEA12935190 | location_locality | San Diego | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:CA:San Diego |
| SAMEA12935190 | location_region | California | R1 | 0.75 | biosample.attribute:geo_loc_name | USA:CA:San Diego |
| SAMEA12935406 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMEA12935190 | subject_id | BLANK.B4.homebrew.L | R1 | 0.85 | sample.attr.host_subject_id | BLANK.B4.homebrew.L |
| SAMEA12935190 | timepoint_label | 1 | R1 | 0.85 | sample.attr.round | 1 |
Sequencing
2,770 runs over 1,971 samples · mean 0.37 Gbp per run (median 47.2 Mbp, total 1,026.09 Gbp; 2,770 runs with a base count) · layout PAIRED 2,770 · platform ILLUMINA 2,770 · models Illumina NovaSeq 6000 (1,631), Illumina HiSeq 4000 (1,139) · 4% of runs with a Sandpiper profile · first public 2020-10-21 – 2022-02-16
Authors (33)
Shaffer JP first · Marotz C · Belda-Ferre P · Martino C · Wandro S · Estaki M · Salido RA · Carpenter CS · Zaramela LS · Minich JJ · Bryant M · Sanders K · Fraraccio S · Ackermann G · Humphrey G · Swafford AD · Miller-Montgomery S · Knight R last · Schwartz T · Austin GI first · Park H · Meydan Y · Seeram D · Sezin T · Lou YC · Firek BA · Morowitz MJ · Banfield JF · Christiano AM · Pe'er I · Uhlemann AC · Shenhav L · Korem T last
Downloads
PRJEB40903.csv.gz (39.8 KB) · parquet (132.9 KB) — all 1,971 samples, every field with route and confidence · PRJEB40903_determinations.csv.gz (61.4 KB) — 12,592 evidence rows