DNA extraction kit, oral/vaginal/rectal microbiome
Cross-sectional study comparing commercial DNA extraction kits for whole metagenomic sequencing of oral, vaginal, and rectal swab samples from five participants in Austin, Texas, including extraction blanks and mock community controls. machine-written summary
79 samples · 158 runs · Age unknown · 2023 · 7.01 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 | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – 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 | 0 | 0% | ||||
| subject_id | 0 | 0% |
- Comparison of commercial DNA extraction kits for whole metagenome sequencing of human oral, vaginal, and rectal microbiome samples 2023 own_data
Archive description
The purpose of this study was to evaluate if systematic differences occur when different commercially available DNA extraction kits are used for whole metagenomic sequencing (WMS) analysis of the human microbiome. Oral, vaginal, and rectal swabs were collected in replicates of four by a healthcare provider from five participants and randomized to one of four DNA extraction kits. Two extraction blanks and three replicate mock community samples were also extracted using each extraction kit. WMS was completed with NovaSeq 6000 for all samples.
How this project entered the registry
Classified as human oral cavity / vaginal / urogenital / gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.scientific_name · “human metagenome”
- body site study.title · “human oral, vaginal, and rectal microbiome”
- body site study.description · “Oral, vaginal, and rectal swabs were collected”
Sequencing
158 runs over 79 samples · mean 3.15 Gbp per run (median 3.51 Gbp, total 497.34 Gbp; 158 runs with a base count) · layout PAIRED 158 · platform ILLUMINA 158 · models Illumina NovaSeq 6000 (158) · 87% of runs with a Sandpiper profile · first public 2023-06-12
Authors (0)
No author record.
Help complete this project
4 of the 4 core fields are below 50% coverage: age_category, country, health_condition, subject_id. Share metadata
Downloads
PRJNA967723.csv.gz (2.4 KB) · parquet (70.9 KB) — all 79 samples, every field with route and confidence · PRJNA967723_determinations.csv.gz (168 B) — 0 evidence rows