NIST RM 8376 spike-in controls in CSF and stool matrices
53 samples from Gaithersburg, Maryland, USA, using NIST Reference Material 8376 bacterial DNA spiked into simulated cerebrospinal fluid and stool to assess metagenomic workflow limit of detection and strain discrimination. machine-written summary
53 samples · 53 runs · US · Age unknown · 2024 · 0.20 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 318 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked · PMC11960059 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
design observational_with_procedure · NIST RM 8376 spike-in of bacterial DNA into stool/CSF samples
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 53 | 100% | 53 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 53 | 100% | 53 | |||
| detailed_location | 53 | 100% | ||||
| latitude | 53 | 100% | 53 | |||
| location_locality | 53 | 100% | 53 | |||
| location_region | 53 | 100% | 53 | |||
| longitude | 53 | 100% | 53 |
- Analytical assessment of metagenomic workflows for pathogen detection with NIST RM 8376 and two sample matrices. 2025 PMID 40062856 PMC11960059 own_data
Archive description
Reference materials were used as spike-in controls for different biological samples (stool and cerebral spinal fluid) to study limit of detection, linearity of response, and ability to discriminate different strains using different metagenomic analysis tools.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.55. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “stool and cerebral spinal fluid”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN40217529 | collection_date | 2022 | R1 | 0.90 | biosample.attribute:collection_date | 2022 |
| SAMN40217529 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Maryland, Gaithersburg |
| SAMN40217529 | latitude | 39.1380 | R1 | 0.90 | biosample.attribute:lat_lon | 39.138 N 77.217 W |
| SAMN40217529 | location_locality | Gaithersburg | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Maryland, Gaithersburg |
| SAMN40217529 | location_region | Maryland | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Maryland, Gaithersburg |
| SAMN40217529 | longitude | -77.2170 | R1 | 0.90 | biosample.attribute:lat_lon | 39.138 N 77.217 W |
Sequencing
53 runs over 53 samples · mean 0.20 Gbp per run (median 0.20 Gbp, total 10.75 Gbp; 53 runs with a base count) · layout PAIRED 53 · platform ILLUMINA 53 · models Illumina MiSeq (53) · 0% of runs with a Sandpiper profile · first public 2024-03-03
Authors (6)
Kralj JG first · Servetas SL · Forry SP · Hunter ME · Dootz JN · Jackson SA last
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJNA1074773.csv.gz (2.1 KB) · parquet (71.2 KB) — all 53 samples, every field with route and confidence · PRJNA1074773_determinations.csv.gz (2.2 KB) — 318 evidence rows