DNA vs RNA vs total NA metagenomics, clinical specimens
96 samples of diverse human clinical specimens (bronchoalveolar lavage, throat swabs, blood, cervical swabs, stool) from China, with matched process controls, comparing DNA-based, RNA-based, and total nucleic acid library preparation workflows for metagenomic sequencing. machine-written summary
96 samples · 192 runs · CN · Age unknown · 2026 · 1.69 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 480 sample values (collection date, country, latitude, location region, longitude) |
| ○ 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 | 96 | 100% | 96 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 96 | 100% | 96 | |||
| detailed_location | 96 | 100% | ||||
| latitude | 96 | 100% | 96 | |||
| location_region | 96 | 100% | 96 | |||
| longitude | 96 | 100% | 96 |
- Library strategies differentially shape microbial, functional, and host signals in clinical metagenomic sequencing. 2026 PMID 42734361 own_data
Archive description
This BioProject contains host-depleted metagenomic sequencing reads generated from diverse human clinical specimens, including bronchoalveolar lavage fluid, throat swabs, blood, cervical swabs, and stool, together with matched process controls. The study was designed as a strictly controlled within-sample comparison of three library preparation workflows: DNA-based libraries, RNA-based libraries, and total nucleic acid libraries. The goal is to evaluate how library chemistry influences microbial detection and overall signal composition across different clinical sample types, including recovery of DNA and RNA pathogens and interpretation of metagenomic sequencing results. These data provide a benchmark resource for methodological comparison and for the development, validation, and interpretation of clinical metagenomic sequencing workflows
How this project entered the registry
Classified as human lower respiratory / oral cavity / blood / tissue / internal fluids / vaginal / urogenital / gut / stool / nasal / nasopharyngeal mixed assays of age unknown by sonnet_x2 with confidence 0.57. Assay mixed.
- host run.host_tax_id · “9606”
- body site study.description · “bronchoalveolar lavage fluid, throat swabs, blood, cervical swabs, and stool”
- body site run.scientific_name · “human lung metagenome”
- body site run.scientific_name · “human oral metagenome”
- body site run.scientific_name · “human blood metagenome”
- body site run.scientific_name · “human vaginal metagenome”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN57106856 | collection_date | 2022/2024 | R1 | 0.90 | biosample.attribute:collection_date | 2022/2024 |
| SAMN57106856 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China |
| SAMN57106856 | latitude | 30.5833 | R1 | 0.90 | biosample.attribute:lat_lon | 30.5833 N 114.2667 E |
| SAMN57106856 | location_region | Hubei | R1 | 0.60 | biosample.attribute:lat_lon | 30.5833 N 114.2667 E |
| SAMN57106856 | longitude | 114.2667 | R1 | 0.90 | biosample.attribute:lat_lon | 30.5833 N 114.2667 E |
Sequencing
192 runs over 96 samples · mean 2.62 Gbp per run (median 0.74 Gbp, total 503.46 Gbp; 192 runs with a base count) · layout PAIRED 192 · platform ILLUMINA 192 · models Illumina NovaSeq 6000 (192) · 0% of runs with a Sandpiper profile · first public 2026-06-02
Authors (0)
No author record.
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJNA1445946.csv.gz (3.1 KB) · parquet (73.2 KB) — all 96 samples, every field with route and confidence · PRJNA1445946_determinations.csv.gz (2.9 KB) — 480 evidence rows